Tag: GOseq

Wallenius Vs Fisher’s Noncentral Hypergeometric Distribution

I’ve found myself in the situation where goseq fails with some relatively extreme numbers (derived from ChIP-Seq data with extreme changes in the IP target) and have tracked it down to the calls to pWNCHypergeo() library(BiasedUrn) pWNCHypergeo(x = 643, m1 = 643, m2 = 16976, n = 17611, odds =…

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Pathway analysis of RNAseq data using goseq package

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

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A command line tool to generate sequence diagrams

A small command line utility used to generate UML sequence diagrams from a text-base definition file. Inspired by js-sequence-diagram and websequencediagram. Install To install it: go get github.com/lmika/goseq To allow automatic generation of PNG files, build with the im tag (ImageMagick is required): go get -tags im github.com/lmika/goseq Usage goseq…

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Bioconductor – rgsepd

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see rgsepd. Gene Set Enrichment / Projection Displays Bioconductor version: 3.4 R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential…

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