Name | Bundle | Description |
---|---|---|
ACGHnorm | microarray | Normalizes two channel array CGH data with LOESS, median or mode. |
ACGHsegment | microarray | Segments Array CGH data with the Circular Binary Segmentation (CBS) algorithm and produces hard or soft copy number aberration calls. |
AdaptorRemoval | sequencing | Removes tags from the reads in fastq/fasta files. |
AffyReader | microarray | Imports gene expression or exon array data from Affymetrix CEL-files. |
AgilentReader | microarray | Imports data from microarray text files such as Agilent CSV files. |
AligFilterFlag | sequencing | Allows to filter SAM files with alignments using the flag field. |
AligFilterMatches | sequencing | Allows filtering of alignments in BAM/SAM files, mainly output from Tophat. |
Align | sequencing | This component aligns sequencing reads to the reference genome using the Borrows-Wheeler aligner with the mem algorithm. Complete documentation: . |
AlleleCounter | microarray | Calculates genotype frequencies of a SNPMatrix. |
AlphaShape | anima | Takes a list of points and returns the alpha shape. |
AnnotateDrugs | dsrt | Annotate drug concentrations. |
Annovar | sequencing | The component annotates genetic variants using ANNOVAR (table_annovar). |
AnnTools | sequencing | Runs one of the AnnTools variant annotator suite's scripts. |
Ant | tools | Anduril wrapper for Apache Ant. |
Array2CSV | builtin | Reads an array, and returns a CSV with Key and File columns. |
Array2Folder | builtin | Transforms an array into a physical folder. |
ArrayCombiner | builtin | Combines multiple arrays into one using set operations on array keys. |
ArrayConstructor | builtin | Constructs an array from atomic elements. |
ArrayExtractor | builtin | Extracts elements from an array. |
ArraySplit | builtin | Divides array keys evenly in to N arrays. |
ArrayTransformer | builtin | Transform arrays by removing elements, renaming keys or sorting the elements. |
Ascat | microarray | Runs Allele specific copy number analysis with ploidy and tumor purity estimation using the tool ASCAT. |
AttributeVisualizer | microarray | Visualizes multidimensional attributes using a heat map together with a clustering dendrogram. |
AutoGating | flowand | Automatically gate cell populations. |
BackgroundSubtract | anima | Performs background subtraction for a directory of images with various methods. |
BackSPIN | tools | Biclustering of gene expression data using the BackSPIN algorithm. |
Bam2Counts | sequencing | Converts Bam files to count matrices summarizing on gene, transcript or exon level. |
Bam2Fastq | sequencing | Revert BAM file to Fastq file for realignment. |
BamCombiner | sequencing | Merges multiple bam files using the Picard MergeSamFiles. |
BashEvaluate | tools | Executes a Bash script that generates any output from the given data or other inputs. |
BayesianBiclustering | tools | Perform Bayesian Biclustering on a data matrix. |
BFConvert | anima | Wrapper for the Bioformats command line tool for converting exotic image formats. |
BFMetadata | anima | Wrapper for the Bioformats command line tool for extracting metadata from exotic image formats. |
BiclustClusterer | tools | TODO. |
BICseq | sequencing | Detects copy number alterations from whole-genome sequencing data using BICseq
tool. |
BiomartAnnotator | microarray | Fetches attributes with given filters using BioMart. |
BismarkAlign | sequencing | Performs alignment of bisulfite sequencing data in addition to deduplication
and methylation extraction using Bismark Bisulfite Mapper . |
Blast | sequencing | Basic local alignment search tool. |
BlobDraw | anima | Visualizes the blobs found in a directory of images. |
BlobFeatures | anima | reads the blobs found in a directory of images and produces intensity features The component requires that all the columns from ImageBlobDetect are still found in the data file. |
BoxPlot | tools | Creates box plots for numeric data. |
BreakpointVisualizer | sequencing | Visualizes genomic breakpoints resulting from copy-number aberrations (amplifications and deletions) and chromosomal rearrangements (translocations and inversions). |
BSAlign(Deprecated) | sequencing | Aligns BS or RRBS data though BSMAP software, version 2.74. |
CellGrowthAssay | dsrt | Compute the plate statistics for the plate survival assays and for dummy plates. |
CellProfiler | anima | Runs a pipeline in CellProfiler, for a folder or several folders of images. |
CGHubDownload | sequencing | Executes CGHub's GeneTorrent package's utilities. |
CircosPlot | microarray | Draws circos plots from genomic data. |
ClassifierPerformance | tools | Calculates popular classifier performance values based on actual classes, and predicted values. |
ClickImage | anima | Get user to click points on a folder of images, and write a CSV table of the coordinates. |
ClusterChooser | flowand | Graphical tool for cluster population selection. |
ClusterFiltering | flowand | Filters columns and/or rows from by clusters using flexible criteria. |
ClusterPlotCombiner | flowand | Creates scatter, line or bar plots where Y and X coordinates come from CSV files. |
ClusterReorder | tools | Re-orders cluster ID numbers based on a given data vector. |
ClusterReport | tools | Performs a hierarchical clustering of samples. |
CN2GECollection | microarray | Encapsulates three algorithms with similar inputs for copy number to RNA expression integration. |
CNACaller | microarray | Calls significant copy number alterations from a group of segmented copy number alteration profiles. |
CNGEIntegrator | microarray | Performs one of two possible nonparametric tests for the detection of copy number induced differential gene expression. |
CombinationCounter | tools | Count the occurrencies of combinations of two labels. |
CombinationMatrix | dsrt | Compute the plate statistics for the plate survival assays and for dummy plates. |
CompareImage | tools | Compare images. |
ControlsQCs | dsrt | Compute the plate statistics for the plate survival assays and for dummy plates. |
ConvertImage | anima | Reads various image formats with LOCI Bioformats library (http://www.loci.wisc.edu/software/bio-formats). |
CopyOutput | builtin | Copies any input to a user selected path. |
CorrelationReport | tools | Creates a correlation report that shows how much columns of a numeric matrix correlate with each other. |
CreateSQLiteDB | sequencing | Create miRNA-target gene database(s) for fast and simple SQLite query of potentially interesting regulatory pairs. |
CreateSQLiteIDs | sequencing | For a subset of genes, create a file with additional reference IDs. |
CSV2Array | builtin | Reads a CSV, and returns an array based on selected columns. |
CSV2Excel | tools | Converts a file from CSV format to Excel 97 format. |
CSV2FASTA | microarray | Converts the given comma separated value file to a FASTA file. |
CSV2GraphML | tools | Converts a matrix or CSV representation of a graph to GraphML. |
CSV2IDList | tools | Extracts columns from each given CSV file and prints their content out without duplicates. |
CSV2Image | anima | Create an image visualization from CSV file. |
CSV2JSON | tools | Transforms a CSV file to JSON format. |
CSV2Latex | tools | Converts the given comma separated value file to a LaTeX table. |
CSV2SetList | tools | Extracts identifier columns from the given CSV files and prints them out without duplicates. |
CSVCleaner | tools | Cleans up CSV outputs, optionally removes file headers, quotations and unused columns, and can reorder and rename columns. |
CSVColRename | tools | Changes column names in a CSV file given a reference file. |
CSVDplyr | tools | Applies up to R functions (including dplyr functions) to the input csv1. |
CSVFilter | tools | Filters columns and/or rows from CSV files using flexible criteria. |
CSVJoin | tools | Joins rows from two or more CSV files from all the inputs, optionally using one column as a matching key. |
CSVListFilter | flowand | Filters CSV files in a given folder according to the to extract specific rows given output of AutoGating component. |
CSVListJoin | tools | Combines the content of input files into a single CSV file. |
CSVSort | tools | Sorts and merges CSV files. |
CSVSplit | tools | Divides the content of the given CSV to an array of multiple CSV files. |
CSVSplitColumns | tools | Splits CSV into new files according to columns. |
CSVSummary | tools | Summarises values for rows of a file according to a column label or the whole file to single row. |
CSVTransformer | tools | Transforms CSV files using R expressions. |
Cuffcompare(Deprecated) | sequencing | Cufflinks includes a program that you can use to help analyze the transfrags you assemble. |
Cuffdiff(Deprecated) | sequencing | Cufflinks includes a program, "Cuffdiff", that you can use to find significant changes in transcript expression, splicing, and promoter use. |
Cufflinks(Deprecated) | sequencing | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. |
Cuffmerge(Deprecated) | sequencing | Cufflinks includes a script called cuffmerge that you can use to merge together several Cufflinks assemblies. |
DEan | sequencing | Performs differential expression analyses in R between pairs of sample groups using up to 4 methods: DESeq, DESeq2, EdgeR, and upper-quartile normalization with t-test. |
DEE2DEG | microarray | Find differentially expressed genes (DEG) based on differentially expressed exons (DEE). |
DEGReport | microarray | Creates a LaTeX report on differentially expressed genes (DEGs). |
DESeqExpr | sequencing | Provides a gene expression matrix using DESeq. |
DiffMeth(Deprecated) | sequencing | Function to compute differential methylation at a base/window/region resolution. |
Directed2Undirected | tools | Converts a directed graph into undirected graph. |
DMML | sequencing | Identifies differentially methylated sites in tumor samples with varying, unknown tumor cell fraction using a maximum-likelihood method. |
DSRTplots | dsrt | Plots the inhibition curves for each screening experiments, combine plots for different pretreatment times and computes the scores indicating the efficacy of each drug. |
DuplicateMarker | sequencing | Mark PCR and optical duplicate reads in BAM files using Picard MarkDuplicates. |
DuplicateQuality | microarray | Estimates microarray chip quality by printing expression distributions for duplicate probes. |
EdgeR | sequencing | Computes the digital expression fold change and p-value based on counts. |
Ellipse2Mask | anima | Converts a CSV expression of ellipses in to masklist (and mask) image format. |
EncodeTextFile | tools | Convert general text files from one character encoding to another. |
EnsemblDNA | microarray | Fetches DNA sequences from the Ensembl database. |
EnsembleAttributeSelection | tools | Feature selection with multiple algorithms. |
EntrezAnnotator | microarray | Retrieves database records from NCBI Entrez, including gene annotation, PubMed references and sequences. |
Excel2CSV | tools | Converts a Microsoft Excel sheet to a CSV file. |
Excel2Text | tools | Converts an Excel 97 xls-sheet to a text file. |
ExclusiveCombiner | tools | Binds one set of inputs to the output ports. |
ExonAnnotator | microarray | Maps gene, transcript or exon Ensembl IDs to one another via the Ensembl query interface. |
ExonExpression | microarray | Converts exon expression matrix for a list of exons of interest. |
ExonToPeptide | microarray | Fetches exon-peptide sequences of query exon list. |
ExpandCollapse | tools | Converts between the two possible representations of a relations with multivalued columns. |
ExperimentSetup | microarray | Creates a report that displays all sample groups using a table and a graph that visualizes the sample groups and their relations. |
ExpExpIntegration | microarray | Integrates gene/transcript/other expression data with binary explanatory data derived in some way. |
ExpressionExtremes | microarray | Selects differentially expressed genes using expression values as criterion. |
ExpressionQuantifier | sequencing | Quantifies expression from a bam file from RNA-Seq. |
ExpressionStats | sequencing | Given an expression matrix and a CSV containing sample IDs and treatment groups, calculate basic statistics by treatment group: mean, median, and standard deviation of genes. |
ExpressionSubset | sequencing | Given an expression matrix and a CSV containing a subset of interest in one column (e.g. |
ExprMethylCGH | microarray | Integrates expression data with methylation and CGH data by using two label matrices of ones and zeros. |
ExprMixtureModel | microarray | Provides a mixture model fit of two normal distributions for the given genes. |
ExtensiveCSVJoin | tools | Combines and cleans many files. |
ExtractCond | sequencing | Creates a custom input file defining treatment groups for MDSPlot component using expression matrices and a reference file. |
FASTA2CSV | sequencing | Converts a FASTA file to CSV. |
FastQC | sequencing | Short reads quality control for high-throughput sequencing data. |
FastQScreen | sequencing | FastQScreen allows you to screen a library of sequences in FastQ format against a set of sequence databases, for example vectors, virus or ribosomal RNA, so you can see if the composition of the library matches with what you expect. |
FCSReader | flowand | FCSReader imports a FCS file (standards 2.0 and 3.0 supported) and converts it into a tab-delimitted CSV file. |
Fiji | anima | Executes a Jython script under Fiji (ImageJ) that generates an image directory from given image directories. |
FijiFeatures | anima | Uses Fiji to extract features from input images, segmented with masks. |
FillNA | tools | Fills NA values with linear interpolation or previous value. |
FlowClustModeling | flowand | Modeling FACS data using flowClust library. |
FlowMeans | flowand | Clusters rows in CSV files. |
FoldChange | microarray | Selects differentially expressed genes using fold change as criterion. |
Folder2Array | builtin | Constructs an array from folder contents. |
FolderCleaner | tools | Renames a folder of files, by leaving only the last extension. |
FolderCombiner | tools | Copies files from input folders to output folder. |
FolderExtractor | tools | Extracts files from a folder. |
FolderSplit | tools | Divides files evenly from a folder in to N folders in an array. |
FSomMetaClustering | tools | Creates self-organizing maps of cytometry data with FlowSOM algorithm and meta clusters the data based on 100 fSOM-maps with consensus clustering. |
FusionAnalyzer | sequencing | Post-processing tool for gene fusion analysis. |
FusionCaller | sequencing | Gene fusion detection. |
FusionGenes(Deprecated) | sequencing | Allows filtering of alignments in BAM/SAM files, mainly output from Tophat. |
FusionVisualizer | sequencing | Post-processing tool for fusion transcripts visualization. |
GatingSummary | flowand | Generate summay report table and heatmap. |
GeneCount | microarray | Produces a LaTeX report that shows the number of genes or features under analysis in various phases of an Anduril script. |
GeneInfo | microarray | Prints detailed information on single genes. |
GeneTable | microarray | Compiles gene ID sets into CSV files that contain gene annotations and expression. |
GenomeSlider | sequencing | Summarized genomic events at sliding window intervals and/or at predifined regions. |
GenomeSpy | microarray | Generates an RMarkdown report, which displays genomic regions or copy number segmentations using GenomeSpy. This component exposes a simplified GenomeSpy API and is limited to displaying only one type of data at a time. |
GenomicRearrangement | sequencing | Call genomic rearrangments. |
GenotypeComparator | microarray | Compares the allele and genotype differences between two sets of genotype frequencies. |
GetReads | sequencing | Visualizes reads that are aligned to a given position. |
GetUtrSeq | sequencing | Fetch UTR sequences of query transcripts. |
GlobalCorrelation | sequencing | Compute correlation between miRNA and gene/transcript expression. |
GMLVQClassifier | tools | Trains a classifier based on the given sample data, or predicts with a classifier trained earlier. |
GNUPlot | tools | Executes a GNUPlot script that generates any output from the given data or other inputs. |
GOClustering | microarray | Clusters genes based on their gene ontology (GO) annotations. |
GOEnrichment | microarray | Computes enriched GO terms in a set of genes or proteins. |
GOFilter | microarray | Filters gene lists based on Gene Ontology annotations. |
GOProbabilityTable | microarray | Creates custom a priori probability tables for GO similarity and enrichment analysis. |
GOSearch | microarray | Filters gene lists based on Gene Ontology annotations. |
GraphAnnotator | tools | Inserts or extracts attributes from GraphML files using CSV files. |
GraphMetrics | tools | Computes various graph metrics for a GraphML file. |
GraphSplitter | tools | Splits a graph into subgraphs that are either connected or strongly connected (case of directed graph) components. |
GraphVisualizer | tools | Creates a visualization of a graph using Graphviz. |
GroupFiles | tools | Produces a CSV annotated by parsing path names containing named groups. |
GSEAAnalyzer | microarray | Performs Gene Set Enrichment Analysis by using category definitions from KEGG or GO. |
GSVDIntegrator | microarray | Extracts variation patterns from two matrices based on the generalized singular value decomposition. |
GTFParser | sequencing | Extracts field contents from a GTF file to output a CSV file. |
GUIInput | builtin | Asks user for inputs. |
HazardRatio | sequencing | Calculates incidence rates, hazard ratios, their CIs and P values. |
HeatMapReport | tools | Clusters samples hierarchically and draws the corresponding dendrograms and heat map. |
HistogramPlot_FrequencyCalculator | tools | Calculates frequencies from data to be used in a HistogramPlot. |
HTMLCombiner | tools | Combines a HTML page from parts. |
HTMLExtractor | tools | Extracts HTML parts from a site. |
HTMLImages | tools | Creates a static list of images to a web page. |
HTMLReport | tools | Visualizes CSV files and their relationships using statically generated HTML files. |
HTMLTable | tools | Creates an interactive HTML table of input data. |
HTSeqCount | sequencing | Quantify reads mapped to EnsemblID transcripts for a given sample. |
HTSeqExprMatrix | sequencing | Takes a CSV list of outputs from HTSeqCount to merge into an expression matrix. |
HTSeqExprNormalize | sequencing | Takes as input "raw", integer count expression matrix of quantified sequenced reads and outputs a scale-normalised, log-transformed expression matrix. |
IDConvert | tools | Converts IDs from a column in a CSV file to other type of IDs and/or combines duplicated rows into one. |
IDDistribution | tools | Extracts one column from the given CSV file and prints the frequencies of its values. |
IlluminaAnnotator | microarray | Fetches genomic annotations for Illumina methylation and expression array probes. |
IlluminaNormalization | microarray | Performs between array normalization for an input matrix. |
IlluminaPlot | microarray | Produces quality control plots. |
IlluminaReader | microarray | Imports gene expression data from Illumina BeadStudio output files. |
Image2CSV | anima | Create a CSV file from image file. |
ImageGallery | anima | Creates a web gallery from given folders of images and optional annotation CSV files. |
ImageList2MaskList | anima | Convert from ImageList type to MaskList data type. |
ImageList2Video | anima | Uses either ImageMagick or avconv to convert a list of images in to a video file. |
ImageLocalMaxima | anima | Finds local maxima centers in a grayscale intensity image. |
ImageMagick | anima | A versatile wrapper for using ImageMagick convert, for folder(s) of images. |
ImageSummary | anima | Summarises a directory of images, with one line for each image. |
INPUT | builtin | Imports an external input file or directory to the pipeline. |
IntensityCorrelation | anima | Extracts the intensity correlation features (Co-Localization) from two image channels. |
IntensityFeatures | anima | Extracts the intensity features from segmented image mask and gray scale image. |
ISABiclust | tools | Does Biclustering using iterative signature algorithm-package. |
iSeq | sequencing | Wraps the iSeq R package that implements the methods described in "A fully Bayesian hidden Ising model for ChIP-seq data analysis" by Qianxing Mo. |
JASPARMotif | microarray | Writes JASPAR motif matrices into a MotifSet directory. |
JCSVJoin | tools | Java implementation of R CSVJoin component. |
KaplanMeier | tools | Produces a Kaplan-Meier plot representing survival estimates based on the given data. |
KaplanMeierPlot | tools | Plots Kaplan Meier survival plot using the survival and survminer R packages. |
KeywordMatcher | microarray | Identifies gene/protein IDs using fuzzy keyword matching between gene aliases and descriptions. |
KGML2GraphML | microarray | Converts a KEGG pathway (KGML) to a GraphML file. |
KorvasieniAnnotator | microarray | Converts gene, transcription, and translation identifiers using Korvasieni. |
Labels2Columns | tools | Reads columns of data, the unique entries of the label column are transposed as column names. |
LatexAttachment | tools | Constructs a LaTeX fragment that includes attachments for the given files. |
LatexCombiner | tools | Combines several LaTeX fragments into one LaTeX document. |
LatexPDF | tools | Compiles a LaTeX document into Portable Document Format (PDF). |
LatexTemplate | tools | Creates LaTeX header and footer files that are inserted to the beginning and the end of the LaTeX report. |
LiftOver | microarray | Converts chromosome region coordinates from one genome build to another. |
LimmaNormalizer | microarray | Normalizes two-channel and single-channel microarrays using the Bioconductor Limma package. |
LimmaStat | microarray | Select differentially expressed probesets, exons or transcripts from probeset, exon or transcript expression data by using limma statistical test. |
LinearBinner | tools | A very basic clustering-like method. |
LinearNormalizer | tools | Normalizes the input matrix column-wise. |
LineFeatures | anima | Measure LinkedList segments as objects. |
LocationVariation | microarray | Gets variation from Ensembl from a genomic location. |
Logo | microarray | Generates sequence logos for the given DNA motifs. |
MACS | microarray | Finds peaks from aligned short-reads. |
MarkerCorrelations | microarray | Combines correlating markers from the SNPMatrices. |
MaskClusterDraw | anima | Reads cluster id:s, images and masks to create a colored visualization of object clustering. |
MaskFilter | anima | Filters mask objects based on the object numbers present in a table. |
MaskList2ImageList | anima | Copy files from MaskList image structure to conventional ImageList data type. |
MaskRelate | anima | Relates objects from two masks defining parents and their children objects. |
MatlabEvaluate | tools | Executes a Matlab script that generates a matrix from the given data. |
MatlabOp | anima | Executes a Matlab script that generates an image directory from given image directories. |
MatrixRank | tools | Computes ranks of values in a matrix. |
MatrixTranspose | tools | Transposes a matrix. |
MDSPlot | tools | Plots multidimensional scaling of numeric data. |
MeapNormalization | microarray | Prepares normalized data at probe level. |
MeapQuantification | microarray | Quantify expression data on exon, splicing variant or gene level. |
MeapVisualizer | microarray | Generate visualization for genes of interest with spliced isoforms. |
MEMERunner | microarray | Finds enriched motifs from the given set of DNA sequences. |
MergeImage | anima | Joins grayscale images together with colors of choice. |
MetaClustering | flowand | Meta-Clustering for defining isomorphisms on cells across clusters. |
MethFilterNorm(Deprecated) | sequencing | Function loading the methylation calls data into a MethylRaw or MethylRawList object (MethylKit package data types)
and performing normalization and filtering of the data. |
MethylCall | sequencing | Perform Methylation Calling of aligned RRBS and WGBS data obtained from the component BSalign.
WARNING: It requires quite a big amount of CPU (For human genome, needs ~26GB memory or more). |
MethylExtract | sequencing | Extracts methylation from a bam file simultaneously with variant calling. |
MicroplateReader | dsrt | Reads multiple XLSX files generated by a fluorescence/luminescence reader for a 96 or 384 well plate and converts it into a tab-delimitted CSV file with the correct annotations for each well. |
MirMatch | sequencing | String match for between mature miRNA seeds and target UTR seeds. |
MMClustering | flowand | Normal, t, Skew-normal, and skew-t Mixture-Model Clustering. |
ModelicaCompiler | tools | Compile a Modelica model into binary form using OpenModelica. |
ModelicaSimulator | tools | Simulate a Modelica model by executing a compiled model. |
MorphologyFeatures | anima | Extracts the morphology features from segmented image mask. |
MotifMatch | microarray | Aligns the given motifs against the DNA sequencies. |
MRXSConvert | anima | Exports MRXS images in to PNGs, cropping them to small images. |
MutationContextPlot | sequencing | Draws mutation context plots for sequencing samples. |
NextGene | microarray | Finds the closest gene, exon, or transcript for the given loci. |
NovelMatureSeq | sequencing | Given a set of putative novel miRNA regions (e.g. output from miRanalyzer or miRDeep2), retrieves consensus functional "mature" region that can then be used for predicting target genes (e.g. as input to MirMatch . |
NucleusGenerator | anima | Generates DAPI-like grayscale images with random cell nuclei. |
ObjectFilter | anima | Filters objects based on the object X,Y coordinates and an overlap with a mask image. |
OptimalClustering | flowand | The component takes the output of the MMClustering component, where each data sample has been clustered with multiple different cluster numbers, and determines the optimal cluster number for each sample. |
OUTPUT | builtin | Exports a result file or directory to an output directory. |
PairCorrelation | tools | Calculates correlations for the row pairs. |
PairWiseClusterPlot | flowand | Produces pairwise scatter plots from clustered and filtered data. |
Pandoc | tools | Executes Pandoc with user given switches. |
PanelDoc | microarray | Calls CNV ratios/gains/losses using the existing programs PanelDoc (developed by Nord et al. 2011) or CNVPanelizer (Bioconductor package), or both, with custom filtering available. |
PanelDoc | sequencing | Calls CNV ratios/gains/losses using the existing programs PanelDoc (developed by Nord et al. 2011) or CNVPanelizer (Bioconductor package), or both, with custom filtering available. |
Pause | builtin | Halts pipeline execution. |
PCA | tools | PCA performs a principal component analysis on a given data matrix based on eigen values. |
PCAxisReader | tools | Converts a PC-Axis file to a CSV. |
PeakScore | microarray | Calculates a cumulative score for each gene having some regions assigned to it. |
PhenographClusterer | tools | Clusters data using Phenograph clustering method. |
PINA | microarray | Finds the interacting proteins of query proteins for a list of query Uniprot ACs. |
PipelineInput | builtin | Read a previous Anduril pipeline execution folder as an input. |
PlateQCs | dsrt | Compute the plate statistics for the plate survival assays and for dummy plates. |
Plink | microarray | Wraps Plink software that allows various genome wide SNP data manipulations and analyzes. |
Plot2D | tools | Creates scatter, line or bar plots where Y and X coordinates come from CSV files. |
PlotChannels | flowand | Component meant to visualize Flow and Mass Cytometry data before and after transformations. |
PlotHTML | tools | Creates scatter, line or bar plots where Y and X coordinates come from JSON files. |
PlotTreeHTML | tools | Produces a plot of a tree (or forest) in a html page. |
PointDistance | tools | Measures the nearest reference point (reference) distance for each input point (in). |
PointTracker | anima | Tracks point coordinates moving in time giving an ID for each track. |
PopulationTimeline | tools | Currently it uses Wanderlust to calculate developmental trajectories within a population of single cell data. |
Properties2Latex | tools | Converts a set of properties files into a LaTeX fragment. |
PyClone | sequencing | Component to run PyClone variant clustering tool. |
PyCloneQC | sequencing | Quality checker for PyClone variant clustering tool. |
PyCloneRC | sequencing | Reclustering tool for PyClone variant clustering. |
PythonEvaluate | tools | Executes an Python script. |
QCParser | sequencing | Parse SeqQC summary result. |
QSNE | tools | Fast nonlinear dimensionality reduction using a quadratic-convergence t-SNE algorithm. |
QuantileFilter | tools | Filters values from numeric matrices that are below or above quantile limits. |
QUBICClusterer | tools | Qualitative biclustering algorithm (QUBIC). https://bioconductor.org/packages/release/bioc/html/QUBIC.html. |
QuickBash | tools | Executes a Bash script that generates any output from the given data or other inputs. |
Randomizer | tools | Generates numeric matrices filled with random values. |
RandomSampler | tools | Randomly selects rows and columns from a text or CSV file without replacement. |
RangeMatch | microarray | Component for 'left join' using keys and ranges. |
RankScore | microarray | Calculates a score matrix for a dichotomially classified set of samples. |
RConfigurationReport | microarray | Generates a report about the versions and the purposes of the selected R packages. |
Realigner | sequencing | This function will do local realignment around indels using Genome Analysis Toolkit (GATK). Complete documentation: . |
RefSNPAnnotator | microarray | Fetches annotations for given SNP rsID's with biomaRt. |
RegionConvert | sequencing | Converts files containing genomic or other sequence related regions to other formats retaining all applicable information. |
RegionReport | microarray | Generates statistics about the DNA regions. |
RegionTransformer | sequencing | Computes DNA region set operations such as union and overlap. |
REvaluate | tools | Executes an R script that generates a matrix from the given data. |
RiskRatioPlot | microarray | Creates a visualization for a list of risk ratios and their confidence intervals. |
RNAFold | microarray | Predicts RNA secondary structure using Vienna RNA Package energy minimization function. |
RowCount | tools | Classifies the number of rows of an input CSV to be either small, medium, or large. |
RowJoin | tools | Joins duplicate id rows from a numeric matrix based on the frequency of some given value. |
Rsync | tools | Uses rsync to fetch or push files. |
RUBIC | sequencing | RUBIC detects recurrent copy number aberrations using copy number breaks, rather than recurrently amplified or deleted regions. |
SampleBalancer | tools | Divides matrix rows in to two, by balancing the occurrence of unique labels in column. |
SampleCombiner | tools | Combines expression data from several samples into one by taking means, medians or log ratios. |
SampleExpression | tools | Creates a -1/0/1 matrix that indicates whether a given gene/probe is differentially expressed in individual samples. |
SampleGroupCreator | tools | Creates sample group tables based on sample names read from data files. |
SamSpectral | flowand | SamSPECTRAL clustering of flow cytometry data as described by Zare et al (2010). |
SBML2GraphML | tools | Visualizes an SBML model as a GraphML file. |
SBML2HTML | tools | Prints the contents of an SBML model as a HTML file. |
SBMLSimulator | tools | Simulates an SBML model using SBML ODE Solver. |
SBMLTable | tools | Extracts SBML attributes into a CSV file, or imports attributes from a CSV file. |
ScalaEvaluate | tools | Executes a Scala script. |
ScalaScript | tools | Scripts Scala source code and executes it via scala.sys.process.Process. |
ScriptIGV(Deprecated) | sequencing | Still under construction! Only the one file input and bedtools igv mode work at the moment, as evidenced by the only test case. |
SearchReplace | tools | Transforms the given file by replacing certain string with new values. |
SegmentBlob | anima | Segment a directory of images with Gaussian Blob method. |
SegmentCRImage | anima | Segments a directory of images with a method tuned for HE images. |
SegmentFiji | anima | Produces binary mask images, segmenting the input images using Fiji. |
SegmentGraphCut | anima | Segmentation based on graph cutting. |
SegmentImage | anima | Segments a directory of images with various methods. |
SegmentPlot | microarray | Plots segmented chromosomal data. |
SegmentSeeded | anima | Segments a directory of images with various methods, using a seed (a previous mask helping in refining the segmentation). |
SelectDiffMeth(Deprecated) | sequencing | Function to select which bases/windows/regions are significantly differentially methylated. |
SelectMethContext | sequencing | Separate cytosines based on the methylation context in which they occur and produces statistics about context methylation. |
SequenceFilter | microarray | Filters out nucleotide sequences that do not satisfy the criteria. |
SequencingRequirements | sequencing | This component depends on the requirements required by the functions in this bundle. |
SetTransformer | tools | Transforms sets using union, intersection, difference and other functions. |
ShapeFitting | anima | Fits a user given shape on image data by changing the location, orientation and scale of the shape. |
SignatureExtractor | sequencing | This component performs signature extraction from point mutation data using non-negative matrix factorization following the pipeline in SomaticSignature R package. |
SignificantCurves | dsrt | Selects drugs based on their efficacy scores. |
SigPathway | microarray | Performs pathway analysis by computing NEk and NTk statistics described in Tian et al (2005). |
SimpleWebPage | tools | Creates a simple web page, for publishing a list of files. |
SISSRs | sequencing | SISSRs is a software application for precise identification of genome-wide transcription factor binding sites from ChIP-Seq data. |
Skeleton2CSV | anima | Extracts lines from a skeleton mask. |
SkeletonFeatures | anima | Extracts intensity information from a grayscale image, using a skeleton mask. |
SNPArrayReader | microarray | Imports genotype data from Illumina SNP and Affymetrix SNP 6.0 or 5.0 files. |
SNPHelistinReader | microarray | Imports genotype data from a SNPHelistin database. |
SNPKaplanMeier | microarray | Calculates Kaplan-Meier estimates for genotype specific survival effects. |
SNPs3DSearch | microarray | Fetches disease associated genes from the SNPs3D database. |
SourceCode2Latex | tools | Converts the given source code to a LaTeX fragment containing the given listing (lstset). |
SpatialContrast | microarray | Finds two spatial regions in expression data that have a maximum contrast in average expression value. |
SpatialPlot | microarray | Creates spatial plots for red/green channels, log ratios and spot quality. |
SPIA | microarray | Performs pathway analysis using Signaling Pathway Impact Analysis (formerly known as Pathway-Express). |
SPINLONG | sequencing | Identify user-defined spatio-temporal patterns in ChIP-seq and other sequencing data using the SPINLONG method. |
SpiralJoin | anima | Joins grayscale images together in a montage, or splits a montage in to separate images in a spiral fashion. |
SPP | sequencing | Wraps the SPP R package from http://compbio.med.harvard.edu/Supplements/ChIP-seq/ published in Kharchenko PK, Tolstorukov MY, Park PJ "Design and analysis of ChIP-seq experiments for DNA-binding proteins" Nat. |
SQLSelect | microarray | Executes an SQL query and returns its results as a CSV file. |
StackProjection | anima | Projects a grayscale z-stack to a 2D image. |
StandardProcess | builtin | Executes a given system command. |
STAR | sequencing | Spliced Transcripts Alignment to a Reference for RNA-seq The reason to implement STAR component was that TopHat is around 50 times slower, and that time is counted in days. |
STARGenome | sequencing | Spliced Transcripts Alignment to a Reference for RNA-seq See the STAR component for more documentation. |
StatisticalTest | tools | Computes p-values using statistical tests, optionally with correction for multiple hypotheses. |
StringInput | builtin | Turns a string into a file usable in the pipeline. |
SubsetBam | sequencing | Extracts reads from a BAM file based on chromosomal regions specified by a user and produces a merged BAM file containing only those regions. |
Summarise | flowand | Summarises values for different rows of a file (i.e. reference) according to the clustered and possibly filtered result of the file (i.e. clusterFiles). |
Summarization | sequencing | Summarizes information from region using sliding window or group ids (same as SQL GROUP BY). When sliding window is used, input file needs to be sorted according to locationCol Variation.jar is in microarray bundle. |
SVDAnalyzer | microarray | Performs Singular Value Decomposition to gene sets to test whether a set of genes is significantly differentially expressed. |
SyntaxHighlight | tools | Reads a program code listing, and creates a syntax highlighted HTML file. |
TableQuery | tools | Executes an SQL query on CSV tables and creates a result table. |
TextDraw | anima | Write text on a bitmap image with a small font. |
TextFileSplitter | tools | Splits a text file (such as CSV) into an array of smaller text files. |
TextureFeatures | anima | The component uses VLFeat library to extract SIFT/MSER keypoints and SIFT descriptors from grayscale images. |
TPquery | sequencing | Retrieve target prediction and target validated data from an SQLite database to annotate a list of miRNAs or a list of miRNA-target gene pairs. |
Transformation | flowand | Cell fluorescense intensity transformation for FACS data. |
Traph | sequencing | Traph RNA-seq abundance estimator from Veli Mäkinen lab. |
TreeSplitter | tools | Splits the leafs of a tree into two sets such that the mutual information between the split and leaf annotations is maximized. |
TrimGalore | sequencing | The component is a wrapper of the trim_galore tool which is also a
wrapper of two tools: fastqc and cutadapt which both should
be in PATH. |
Trimmer | sequencing | Trim sequence reads at both ends. |
Trimmomatic | sequencing | Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. |
TSNE | tools | This component performs dimensionality reduction with an R wrapper of the C++ implementation of Barnes-Hut-SNE as described in http://lvdmaaten.github.io/tsne/. |
TumorscapeReader | microarray | Connects to the Tumorscape database and outputs chromosomal aberration information for the query genes. |
UMIQuantifier | sequencing | Quantifies distinct unique molecular identifiers (UMIs) from a bam file, and performs deduplication in scRNA-seq or targeted sequencing data. |
URLInput | builtin | Imports an external input file to a workflow script from a URL source. |
UtrSeq2Seeds | sequencing | Generate seeds with 15bp (XXXXXXXQXXXXXXX) with each query loci in middle. |
VariantAnnotator(Deprecated) | sequencing | This component is not being actively maintained currently, since Annovar is updated to frequently. |
VariantFilter | sequencing | Filters variants based on allele frequencies in the data. |
VariationFilter | tools | Filters out rows from a matrix where the standard deviation is below (or above) a threshold. |
VCF2AnnotatedCSV | sequencing | A quick and dirty wrapper for ANNOVAR. |
VCF2CSV | sequencing | Converts variation calls in VCF format to CSV. |
VCMM | sequencing | A variant caller, from VCMM website. |
VennDiagram | tools | Draws Venn diagrams showing the intersections of the given sets of identifiers. |
VertexJoin | tools | Simplifies the given graph by merging vertices with an equal set of edges. |
Video2ImageList | anima | Uses either ImageMagick or avconv to convert a list of images in to a video file. |
Watershed | anima | Methods to divide objects in a mask, or grayscale images. |
WekaAPriori | tools | Mines association rules using a priori algorithm: R. |
WekaAttributeSelection | tools | Selects parameters using Weka AttributeSelection classes. |
WekaClassifier | tools | Creates a classifier based on the given sample data. |
WekaClusterer | tools | Clusters data using clustering methods implemented in Weka. |
WekaTransform | tools | Transforms data using filter classes implemented in Weka. |
XML2CSV | tools | Transforms an XML file into CSV table. |
XShiftClusterer | tools | Clusters data using the original implementation of the X-shift algorithm. |
Name | Bundle | Description |
---|---|---|
AffyNormalization | microarray | Reads in Affymetrix gene expression microarrays and compares various normalization methods. |
AffySNPFetch | microarray | Fetches SNP rs-numbers from Ensembl based on Affy SNP-ids. |
AgilentImport | microarray | Imports Agilent microarray data, merges duplicate probes and creates a log ratio matrix. |
AlignStats | sequencing | Evaluate sequencing data, especially RNA-seq data quality using RSeQC. |
AnnotEnsembl | sequencing | Takes the ncRNA fasta file downloaded from Ensembl and creates a gff file with the transcript IDs as the reference chromosome. |
AnnotMirbase | sequencing | Takes a GFF3 file downloaded from miRBase and modifies the genomic locations to reference by Ensembl transcript ID (instead of chromosome) and relative positions inside the transcript ID (start and end positions). |
AssemblyQuality | sequencing | Evaluate the quality of a de novo genome assembly using a variety of metrics. |
BamReducer | sequencing | This function reduces the reads in a bam file using the Genome Analysis Toolkit (GATK) 2 and outputs a dramatically more compressed bam file. |
BamRegrouper | sequencing | Picard-tools is used to add or replace read group information for each read in the input alignment file. |
BamReorder | sequencing | This function reorders reads in a BAM file to match the contig ordering in the provided reference file. . |
BamStats | sequencing | The function collects alignment and coverage statistics from a bam file. |
BaseRecalibrator | sequencing | This function will do base quality score recalibration using Genome Analysis Toolkit (GATK). |
ClusterAnnotator | microarray | Produces a hierarchical clustering of the samples and assigns the provided annotations to the brances of the clustering tree. |
ClusterPlot | flowand | Generates 2D plots for clusters where the dimensions are specified, hence specializing the pairwise plotting of all possible pairs of clusters dimensions. |
DataOverlap | sequencing | Take the union of and collapse 2 datasets, with the option to filter out rows with NAs. |
DiffExprSeq(Deprecated) | sequencing | For differential expression at gene and exon level of RNA-Seq data. |
DocumentGenerator | microarray | Creates a PDF document from the given LaTeX elements and of the system configuration. |
EnsemblChromosomes | sequencing | Retrieves the Ensembl names and lengths of chromosomes. |
EnsemblGenes | sequencing | Retrieves the Ensembl gene locations. |
ExpressionImport | microarray | Reads expression data, applies all available normalization methods and returns a record with normalized datasets. |
ExprTable | sequencing | Generates an expression table from individual samples expression files. It was created with genes.fpkm_tracking and isoforms.fpkm_tracking files from Cufflinks in mind, but it can be used to summarize in one table any group of expression files that have an id column common to all files and the expression values. |
ExprTableReport | sequencing | Generates expression statistics into an HTML report. |
FusionMap(Deprecated) | sequencing | Detect genomic fusions from paired or single ended DNA-seq or RNA-seq data using FusionMap. |
GenomicVariantAnnotator | microarray | Queries the Database of Genomic Variants. |
HistogramPlot | tools | Counts the frequencies and makes a line plot of histogram values. |
HTSeqBam2Counts | sequencing | For obtaining read counts at gene and exon level from RNA-Seq alignment files. |
InteractionPlot | microarray | Plots the distribution of the expression of two genes. |
LatexSearchReplace | tools | Transforms text (including Tex) files in the given Latex directory by replacing certain string with new values in the specified text files. |
MicroarrayReader | microarray | Reads in expression microarray data produced by feature extraction software. |
MutSig | sequencing | Determine significantly mutated genes in a set of genetic variations using MutSig. |
NCRNAAnnot | sequencing | Creates reference files for gene features and known ncRNAs and creates additional columns for a putatively novel miRNA expression matrix with information on relative genomic location (e.g. intragenic/intergenic, host gene and transcript) and neighbouring or overlapping ncRNAs. |
NovelExprMatrix | sequencing | Take output of miRanalyzer (or miRDeep2 ) and create an expression matrix with the putative novel miRNAs found. |
NovelMirnas | sequencing | Performs novel miRNA discovery using miRanalyzer or mirDeep2, depending on what is installed and what you want to use. |
PrepRnaBam | sequencing | Preprocessing of RNA bam files according to GATK best practices (adding groups, marking duplicates, splitNtrim and base recalibration). |
QCFasta | sequencing | Quality control function for high-throughput sequencing data. |
QueryReport | tools | Executes an SQL query and prints it with the result table. |
ReferenceIndexer | sequencing | The following auxiliary files for the reference fasta sequence will be created:
|
RegionOverlap(Deprecated) | microarray | Produces a list of overlapping DNA regions. |
RNAVariantCaller | sequencing | Variant calling in RNAseq data using HaplotypeCaller and VariantFiltration in GATK. |
Sam2Fastq | sequencing | This function uses the Picard java library to perform a conversion from SAM/BAM alignment format back to FASTQ sequence format. |
SGA | sequencing | Perform de novo assembly for sequencing reads using String Graph Assembler (SGA). |
SmallRNAPrep | sequencing | Uses FASTX-Toolkit to perform adapter trimming, artifact filtering, base-quality filtering, and read trimming for single-end read data. |
SmallRNAQC | sequencing | Performs all 3 quality filtering steps (preprocessing, alignment to genome, and optional alignment to transcripts) in the smallRNA pipelines. |
Star2Pass | sequencing | Runs STAR aligner in two pass mode for an array of samples together. |
VariantCaller | sequencing | Calls genomic sites of variation using the specified caller. |
VariantCombiner | sequencing | This function combines all input variant files into one file using the Genome Analysis Toolkit (GATK). |
VariantLiftover | sequencing | This is analogous to the LiftOver component, but for VCF files. |
VariantRecalibrator | sequencing | This function will apply machine learning in order to improve the input variants. |
VariantSelector | sequencing | Select variants from a VCF file using specific criteria, e.g. type, annotations or genomic intervals. |
VariantValidator | sequencing | This function validates the input variant file using the Genome Analysis Toolkit (GATK). |