DiffBind

Use when performing differential expression analysis on RNA-seq or count data using baySeq, an empirical Bayesian framework for DE analysis. Covers full workflow: constructing countData objects, estim

1 shared topic • 2 shared operations

Bioconductor ExperimentHub — unified R interface for discovering and downloading global experimental genomics data resources (single-cell RNA-seq, bulk RNA-seq, ChIP-seq, ATAC-seq, proteomics, methyla

1 shared topic • 2 shared operations

mpralm is an R/Bioconductor package for differential activity analysis of Massively Parallel Reporter Assays (MPRA). It uses a limma-voom-style framework to compare RNA barcode counts to DNA barcode c

3 shared operations

PyDESeq2 — Python implementation of DESeq2 for differential gene expression analysis from bulk RNA-seq count data. Performs size factor normalization, genewise dispersion estimation, Wald tests with B

3 shared operations

tximport -- R/Bioconductor package for importing transcript-level abundance, estimated counts, and transcript lengths from quantification tools (Salmon, Kallisto, RSEM, StringTie, Sailfish) and summar

3 shared operations