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Up: Category summary
Category
Expression| Description | Gene expression analysis tools. |
|---|
| Component | Version | Inputs | Outputs | Description |
|---|---|---|---|---|
| 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. |
| DESeqExpr | 1.0 | geneCounts, sampleNames | expr, log2 | Provides a gene expression matrix using DESeq. |
| 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. |
| ExprTable | 1.1 | array, auxiliary | table, log2, topHits, plots | 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 | 1.0 | expr, ref, colLabels, annotation, geneSet, bodyMap | table, expressed, document, report | Generates expression statistics into an HTML report. |
| GlobalCorrelation | 1.2 | gene, mirna | correlated_filtered, correlated_all, expression_miRNA, expression_mRNA | Compute correlation between miRNA and gene/transcript expression. |
| HTSeqCount | 1.0 | bam, annotation_mirbase | counts | Quantify reads mapped to EnsemblID transcripts for a given sample. |
| HTSeqExprMatrix | 0.1 | samples, TPM | countArray, no_feature | Takes a CSV list of outputs from HTSeqCount to merge into an expression matrix. |
| NovelExprMatrix | 1.0 | novelArray | csv, csv_wID | Take output of miRanalyzer (or miRDeep2) and create an expression matrix with the putative novel miRNAs found. |