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ablooper

Tool for modelling the CDRs of antibodies

aging_tcell_tea-seq

Tri-modal single cell profiling reveals a novel pediatric CD8aa T cell subset and broad age-related molecular reprogramming across the T cell compartment.

archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

asap_to_kite

CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing

auto-gpt

An experimental open-source attempt to make GPT-4 fully autonomous.

awesome-single-cell

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

awesome-vdj

📚 Tools and databases for analyzing HLA and VDJ genes.

bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines

bcr-repertoire-papers

Collection of papers related to BCR repertoire analyses

bitfam

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

cell_reports_rat_vta_snrna_2022

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cellphonedb

celltypist

A tool for semi-automatic cell type classification, harmonization and integration

chromvar

chromatin Variability Across Regions (of the genome!)

clustermap

ClusterMap is an R package to analyze and compare two or more single cell expression datasets.

cometsc

COMET Single-Cell Marker Detection tool

covid19-scatac-seq

crossslo_brc_cxcl13

crosstalker

R package to do the Ligand Receptor Analysis Visualization

dandelion

dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data

enclone

VDJ Clonotyping & Analysis Tools

enrichintersect

R package for custom set enrichment analysis (CSEA) and interactive visualization of intersecting sets

ezsinglecell2

gseaplot

gseavis

An implement R package to visualize GSEA results

immunarch

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

liana

LIANA: a LIgand-receptor ANalysis frAmework

liger

Lightweight Iterative Gene set Enrichment in R

mbc_plasticity_moor_boyman_collaboration

This is the code that was used to analyze the single cell sequencing data for the project "Fate and plasticity of SARS-CoV-2-specific B cells during memory and recall in humans"