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

Scope+: An open source generalizable architecture for single-cell atlases at sample and cell levels

p-IgGen: A Generative Paired Antibody Language Model

A curated and summarized list of bioinformatics bench-marking papers and resources.

scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics

Interpretation of cell states using reference single-cell maps

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

Gene regulatory network containing signed transcription factor-target gene interactions

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

Methods to discover gene programs on single-cell data

A library for creating complex UpSet plots with ggplot2 geoms

Paginate the HTML Output of R Markdown with CSS for Print

R package for semi-supervised single-cell data integration

flowchart is an R package for drawing participant flow diagrams directly from a dataframe using tidyverse.

Please download the latest version. "HIVSeqinR" is an R-based pipeline that processes HIV near-full-genome sequences and classifies genomes into "intact" or into various "defective" categories. Ple…

A toolkit for single-cell immune profiling

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

Significance analysis for clustering single-cell RNA-sequencing data

A visualization software for antibody multi sequence alignment

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

https://www.sc-best-practices.org

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..