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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.

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