a-thind

ggstatsplot

Enhancing {ggplot2} plots with statistical analysis 📊📣

ComplexHeatmap

Make Complex Heatmaps

bedtools2

bedtools - the swiss army knife for genome arithmetic

immunedeconv

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods

EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling

fgsea

Fast Gene Set Enrichment Analysis

DESeq2

Differential expression of RNA-seq data using the Negative Binomial

rmats-turbo

sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

GSVA

Gene set variation analysis

ggvenn

Venn Diagram by ggplot2, with really easy-to-use API.

tximport

Transcript quantification import for modular pipelines

eulerr

Area-Proportional Euler and Venn Diagrams with Ellipses

msigdbr

MSigDB gene sets for multiple organisms in a tidy data format

degust

An interactive web-tool for RNA-seq analysis

rnaseqGene

RNA-seq workflow: exploratory analysis and differential expression

sailor

CWL+Singularity implementation of an RNA editing workflow

ConsensusTME

ConsensusTME Gene Sets and R Script

SpatialDecon

The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)

iCount

iCount, protein-RNA interaction analytics

maser

Mapping Alternative Splicing Events to pRoteins

standR

Spatial transcriptomics analyses and decoding in R

PAIRADISE

Paired Replicate Analysis of Allelic Differential Splicing Events

isomiRs

analyze isomiRs from seqbuster tool

CAFclassification

peka

Find motifs enriched around prominent crosslinks

QuickMIRSeq

Integrated and Interactive microRNA-seq Analysis Report

htseq-clip

a toolset designed for the processing and analysis of eCLIP/iCLIP dataset

Decosus

Consensus deconvolution and abudance