edgeR

Use when performing differential gene expression analysis on RNA-seq count data using limma-voom. Covers the full workflow: count filtering with filterByExpr, TMM normalization via edgeR calcNormFacto

1 shared topic • 3 shared operations

Use when working with batchelor — the Bioconductor R package for batch correction of single-cell RNA-seq data. Removes batch effects using mutual nearest neighbours (fastMNN, mnnCorrect), linear resca

2 shared topics • 1 shared operation

GATK4 — Genome Analysis Toolkit for germline and somatic short variant discovery (SNPs and indels). Industry-standard caller providing HaplotypeCaller for germline, Mutect2 for somatic, plus Base Qual

2 shared topics • 1 shared operation

HTSeq — Python framework for high-throughput sequencing data analysis, primarily used for counting aligned reads overlapping genomic features (genes, exons) from SAM/BAM/CRAM files using GTF/GFF annot

2 shared topics • 1 shared operation

Strelka2 — fast and accurate small variant caller for germline and somatic analysis. Detects SNVs and indels (up to ~49 bp) from mapped paired-end sequencing reads with tiered haplotype modeling, adap

2 shared topics • 1 shared operation