Single-cell Transcriptome and Regulome Analysis Pipeline

R/Bioconductor package for working with 10x scATACseq data

Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs

Analysis of physically interacting cells (PICs) in flow cytometry data using R

Scissor package

Publication-ready volcano plots with enhanced colouring and labeling

Demultiplexing pooled scRNA-seq data with or without genotype reference

Peak-based selection of high quality cytometry data

Single-cell immune repertoire trajectory analysis in R

Robust identification of perturbed cell types in single-cell RNA-seq data

R package for analysing single cell data

Methods to discover gene programs on single-cell data

Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning

mgatk: mitochondrial genome analysis toolkit

Highly informative TCR representation model

Inference of TCR motifs

single cell Flux Estimation Analysis (scFEA) Try the below web server!

Easy single cell analysis platform for enrichment

COMET Single-Cell Marker Detection tool

Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.

"ltc_palettes: Tailored for data visualization enthusiasts, ltc_palettes is an R package that offers a curated collection of color palettes. Crafted to enhance clarity and impact, these palettes en…

Cell age determination by scATAC-seq and bulk-ATAC-seq

Large language modeling applied to T-cell receptor (TCR) sequences.

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of m…

Single-Cell Genotyping Tool

R package for using SNPs to QC HTO and LMO demultiplexing calls

Comprehensive pipeline for donor demultiplexing in single cell