| Component |
Version |
Inputs |
Outputs |
Description |
| AnnotEnsembl |
1.0 |
|
annot |
Takes the ncRNA fasta file downloaded from Ensembl and creates a gff file with the transcript IDs as the reference chromosome. |
| AnnotMirbase |
1.0 |
|
annot |
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). |
| Bam2Fastq |
0.1 |
in |
out |
Revert BAM file to Fastq file for realignment. |
| CreateSQLiteDB |
0.1 |
DBlist |
|
Create miRNA-target gene database(s) for fast and simple SQLite query of potentially interesting regulatory pairs. |
| CreateSQLiteIDs |
0.1 |
geneList |
wIDs |
For a subset of genes, create a file with additional reference IDs. |
| DataOverlap |
1.0 |
annot1, annot2 |
annot |
Take the union of and collapse 2 datasets, with the option to filter out rows with NAs. |
| DEan |
0.4 |
expr, treatment |
array, diffExpr |
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. |
| ExpressionStats |
0.1 |
expr, ref, geneSet, bodyMap |
stats, statsArray, report |
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 |
0.1 |
exprMatrix, reference |
subset |
Given an expression matrix and a CSV containing a subset of interest in one column (e.g. |
| ExtractCond |
0.1 |
exprMatrix, reference |
table |
Creates a custom input file defining treatment groups for MDSPlot component using expression matrices and a reference file. |
| GetUtrSeq |
1.0 |
transcripts, connection |
UTR5, UTR3 |
Fetch UTR sequences of query transcripts. |
| GlobalCorrelation |
1.2 |
gene, mirna |
correlated_filtered, correlated_all, expression_miRNA, expression_mRNA |
Compute correlation between miRNA and gene/transcript expression. |
| MirMatch |
1.0 |
utrSeeds, matureSeq, pairs |
matched |
String match for between mature miRNA seeds and target UTR seeds. |
| SmallRNAPrep |
1.0 |
reads |
fastq, stats |
Uses FASTX-Toolkit to perform adapter trimming, artifact filtering, base-quality filtering, and read trimming for single-end read data. |
| SmallRNAQC |
1.0 |
reads, mates, stats, bam, mergeStats |
qc, report, fastqc |
Performs all 3 quality filtering steps (preprocessing, alignment to genome, and optional alignment to transcripts) in the smallRNA pipelines. |
| TPquery |
0.3 |
refTable |
array, annot |
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. |
| UtrSeq2Seeds |
1.0 |
utrseq |
seeds |
Generate seeds with 15bp (XXXXXXXQXXXXXXX) with each query loci in middle. |
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smallRNA