ZheFrench

kBET

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

infercnvPlus

DIALOGUE

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

spotless-benchmark

A repository for benchmarking spatial deconvolution and mapping tools

cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor

Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data

regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

universc

UniverSC: a flexible cross-platform single-cell data processing pipeline

TPMCalculator

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

ggsashimi

Command-line tool for the visualization of splicing events across multiple samples

splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

SingleCellSignalR

R package for Bioconductor submission

r-base-feedstock

A conda-smithy repository for r-base.

covtobed

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

cgpBigWig

BigWig manpulation tools using libBigWig and htslib

Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level

spladder

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.

portcullis

Splice junction analysis and filtering from BAM files

WiggleTools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

RNA-seq-analysis

RNAseq analysis notes from Ming Tang

seqan

SeqAn's official repository.