scRNA-tools

B

BALDR

BALDR is a pipeline for reconstructing human or rhesus macaque immunoglobulin(Ig)/B cell receptor(BCR) sequences from single cell RNA-Seq data generated by Illumina sequencing.

Publications: 1, Preprints: 0, Total citations: 64

Publications
"BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data"
DOI: 10.1186/s13073-018-0528-3, Published: 2018-03-20, Citations: 64

Platform: Perl
Code: https://github.com/BosingerLab/BALDR
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License: MIT
Categories: Alignment, Assembly, Immune
Added: 2018-04-04, Updated: 2018-04-04

BASIC

BASIC is a semi-de novo assembly method to determine the full-length sequence of the BCR in single B cells from scRNA-seq data.

Publications: 1, Preprints: 0, Total citations: 92

Publications
"BASIC: BCR assembly from single cells"
DOI: 10.1093/bioinformatics/btw631, Published: 2016-10-02, Citations: 92

Platform: Python
Code: http://ttic.uchicago.edu/~aakhan/BASIC/
License: MIT
Categories: Assembly, Immune
Added: 2016-10-10, Updated: 2017-09-09

BENISSE

Benisse (BCR embedding graphical network informed by scRNA-Seq) provides a powerful tool for analyzing B cell receptors (BCRs) guided by single cell gene expression of the B cells

Publications: 1, Preprints: 0, Total citations: 17

Publications
"Interpreting the B-cell receptor repertoire with single-cell gene expression using Benisse"
DOI: 10.1038/s42256-022-00492-6, Published: 2022-06-02, Citations: 17

Platform: Python/R
Code: https://github.com/wooyongc/Benisse
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License: MIT
Categories: Dimensionality Reduction, Immune, Visualisation
Added: 2022-06-10, Updated: 2022-06-10

BraCeR

BraCeR - reconstruction of B cell receptor sequences from single-cell RNA-seq data.

Publications: 1, Preprints: 1, Total citations: 89

Publications
"BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq"
DOI: 10.1038/s41592-018-0082-3, Published: 2018-07-31, Citations: 84
Preprints
"BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing"
DOI: 10.1101/185504, Citations: 5

Platform: Python/R
Code: https://github.com/teichlab/bracer
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License: Apache-2.0
Categories: Alignment, Assembly, Immune, Quantification, Visualisation
Added: 2017-09-09, Updated: 2017-08-03

BRAPeS

BRAPeS (BCR Reconstruction Algorithm for Paired-End Single-cell), software for reconstruction of B cell receptors (BCR) using short, paired-end single-cell RNA-sequencing.

Publications: 1, Preprints: 1, Total citations: 10

Publications
"Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS"
DOI: 10.26508/lsa.201900371, Published: 2019-08-26, Citations: 10
Preprints
"Reconstructing B cell receptor sequences from short-read single cell RNA-sequencir with BRAPeS"
DOI: 10.1101/389999, Citations: 0

Platform: Python
Code: https://github.com/YosefLab/BRAPeS
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License: Custom
Categories: Alignment, Immune
Added: 2018-08-24, Updated: 2018-08-24

C

CellaRepertorium

Methods to cluster and analyze high-throughput single cell immune cell repertoires, especially from the 10X Genomics VDJ solution
Platform: R/C++
Code: https://github.com/amcdavid/CellaRepertorium
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License: GPL-3.0
Categories: Clustering, Immune, Quality Control, Variants, Visualisation
Added: 2020-11-29, Updated: 2020-11-29

CoNGA

conga was developed to detect correlation between T cell gene expression profile and TCR sequence in single-cell datasets

Publications: 1, Preprints: 1, Total citations: 97

Publications
"Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA)"
DOI: 10.1038/s41587-021-00989-2, Published: 2021-08-23, Citations: 88
Preprints
"Linking T cell receptor sequence to transcriptional profiles with clonotype neighbor graph analysis (CoNGA)"
DOI: 10.1101/2020.06.04.134536, Citations: 9

Platform: Python
Code: https://github.com/phbradley/conga
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License: MIT
Categories: Clustering, Immune, Visualisation
Added: 2021-09-03, Updated: 2021-09-03

D

DALI

DALI (Diversity AnaLysis Interface): a novel tool for the integrated analysis of multimodal single cell RNAseq data and immune receptor profiling

Publications: 0, Preprints: 1, Total citations: 8

Preprints
"DALI (Diversity AnaLysis Interface): a novel tool for the integrated analysis of multimodal single cell RNAseq data and immune receptor profiling"
DOI: 10.1101/2021.12.07.471549, Citations: 8

Platform: R
Code: https://github.com/vibscc/DALI
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License: GPL-3.0
Categories: Immune, Integration, Visualisation
Added: 2021-12-10, Updated: 2021-12-10

dandelion

dandelion is a python package for analyzing single cell BCR/V(D)J data from 10x Genomics 5' kit

Publications: 2, Preprints: 2, Total citations: 609

Publications
"Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins"
DOI: 10.1038/s41587-023-01734-7, Published: 2023-04-13, Citations: 28
"Single-cell multi-omics analysis of the immune response in COVID-19"
DOI: 10.1038/s41591-021-01329-2, Published: 2021-04-20, Citations: 564
Preprints
"The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres"
DOI: 10.1101/2021.01.13.21249725, Citations: 13
"Dandelionutilizes single cell adaptive immune receptor repertoire to explore lymphocyte developmental origins"
DOI: 10.1101/2022.11.18.517068, Citations: 4

Platform: Python
Code: https://github.com/zktuong/dandelion
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License: AGPL-3.0
Categories: Immune, Visualisation
Added: 2021-02-05, Updated: 2023-05-05

dsb

An R package for normalizing and denoising antibody derived tag (ADT) data from CITE-seq and derivative assays (TEA-seq, ASAP-seq etc.)

Publications: 1, Preprints: 1, Total citations: 112

Publications
"Normalizing and denoising protein expression data from droplet-based single cell profiling"
DOI: 10.1038/s41467-022-29356-8, Published: 2022-04-19, Citations: 93
Preprints
"Normalizing and denoising protein expression data from droplet-based single cell profiling"
DOI: 10.1101/2020.02.24.963603, Citations: 19

Platform: R
Code: https://github.com/niaid/dsb
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License: Custom
Categories: Immune, Normalisation, Transformation
Added: 2021-03-05, Updated: 2023-03-31

E

enclone

Accurate and user-friendly computational tool for clonal grouping to study the adaptive immune system

Publications: 0, Preprints: 1, Total citations: 6

Preprints
"enclone: precision clonotyping and analysis of immune receptors"
DOI: 10.1101/2022.04.21.489084, Citations: 6

Platform: Rust
Code: https://github.com/10XGenomics/enclone
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License: Custom
Categories: Immune
Added: 2022-08-12, Updated: 2022-08-12

G

gExcite

A start-to-end framework for single-cell gene expression, hashing, and antibody analysis

Publications: 1, Preprints: 1, Total citations: 1

Publications
"gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis"
DOI: 10.1093/bioinformatics/btad329, Published: 2023-05-01, Citations: 1
Preprints
"gExcite - A start-to-end framework for single-cell gene expression, hashing, and antibody analysis"
DOI: 10.1101/2022.05.23.490488, Citations: 0

Platform: Snakemake/R/Python
Code: https://github.com/ETH-NEXUS/gExcite_pipeline
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License: GPL-3.0
Categories: Alignment, Differential Expression, Immune, Quantification, UMIs
Added: 2022-05-27, Updated: 2024-01-05

I

Ibex

Using BCR sequences for graph embedding

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"Ibex: Variational autoencoder for single-cell BCR sequencing."
DOI: 10.1101/2022.11.09.515787, Citations: 0

Platform: R
Code: https://github.com/ncborcherding/Ibex
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License: MIT
Categories: Dimensionality Reduction, Immune
Added: 2022-11-11, Updated: 2023-10-20

iBRIDGE

Can integrate and bridge between bulk and single-cell gene expression data types to quantify T cell infiltration levels

Publications: 1, Preprints: 0, Total citations: 2

Publications
"iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-Cell RNAseq Data and Differentiate Cell Type–Specific Markers of Immune-Cell Infiltration"
DOI: 10.1158/2326-6066.CIR-22-0283, Published: 2023-04-06, Citations: 2

Platform: R
Code: https://github.com/tolgaturan-github/IBRIDGE
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Categories: Classification, Gene Sets, Immune, Integration, Normalisation
Added: 2023-05-05, Updated: 2023-05-05

ImmClassifier

Knowledge-based and lineage-driven immune cell classification in single-cell RNA-Seq data

Publications: 1, Preprints: 1, Total citations: 12

Publications
"Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data"
DOI: 10.1093/bib/bbab039, Published: 2021-03-03, Citations: 12
Preprints
"Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier"
DOI: 10.1101/2020.03.23.002758, Citations: 0

Platform: R/Python
Code: https://github.com/xliu-uth/ImmClassifier
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License: GPL-3.0
Categories: Classification, Immune
Added: 2020-04-01, Updated: 2021-03-12

immunarch

Fast and Seamless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires in R
Platform: R/C++
Code: https://github.com/immunomind/immunarch
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License: Apache-2.0
Categories: Immune, Visualisation
Added: 2020-06-26, Updated: 2024-03-22

immunopipe

Integrative analysis for single-cell RNA sequencing and single-cell TCR sequencing data
Platform: Python/R/Shell
Code: https://github.com/pwwang/immunopipe
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License: GPL-3.0
Categories: Clustering, Gene Sets, Immune, Integration, Marker Genes, Visualisation
Added: 2024-04-05, Updated: 2024-04-05

iTALK

iTALK is an R toolkit for characterizing and illustrating intercellular communication

Publications: 0, Preprints: 1, Total citations: 196

Preprints
"iTALK: an R Package to Characterize and Illustrate Intercellular Communication"
DOI: 10.1101/507871, Citations: 196

Platform: R
Code: https://github.com/Coolgenome/iTALK
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License: CC-BY-NC-ND-4.0
Categories: Differential Expression, Gene Networks, Immune, Visualisation
Added: 2019-01-11, Updated: 2019-01-14

L

LRT

The LRT package is an R package for clonotype lineage inference and clustering analysis

Publications: 1, Preprints: 1, Total citations: 5

Publications
"LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity"
DOI: 10.1371/journal.pcbi.1011300, Published: 2023-07-10, Citations: 5
Preprints
"LRT: T Cell Trajectory Inference by Integrative Analysis of Single-Cell TCR-seq and RNA-seq data"
DOI: 10.1101/2022.04.14.488320, Citations: 0

Platform: R
Code: https://github.com/JuanXie19/LRT
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Categories: Immune
Added: 2022-05-01, Updated: 2023-07-14

M

MiXCR

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling. It supports all kinds of single cell platforms and technologies for immune profiling, including commercial vendors such as 10x Genomics or BD Rhapsody and any custom protocol (droplet-based, plate-based, combinatorial barcoding etc.). Check more at https://docs.milaboratories.com.

Publications: 2, Preprints: 0, Total citations: 1632

Publications
"Antigen receptor repertoire profiling from RNA-seq data"
DOI: 10.1038/nbt.3979, Published: 2017-10-11, Citations: 257
"MiXCR: software for comprehensive adaptive immunity profiling"
DOI: 10.1038/nmeth.3364, Published: 2015-04-29, Citations: 1375

Platform: Java/Kotlin
Code: https://github.com/milaboratory/mixcr
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License: Custom
Categories: Alignment, Allele Specific, Assembly, Clustering, Immune, UMIs
Added: 2022-12-25, Updated: 2022-12-25

mvTCR

A multimodal generative model to learn a unified representation across modalities and datasets for joint analysis of single-cell immune profiling data

Publications: 0, Preprints: 1, Total citations: 16

Preprints
"Integrating T-cell receptor and transcriptome for large-scale single-cell immune profiling analysis"
DOI: 10.1101/2021.06.24.449733, Citations: 16

Platform: Python
Code: https://github.com/SchubertLab/mvTCR
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License: MIT
Categories: Dimensionality Reduction, Immune, Integration, Perturbations
Added: 2022-10-28, Updated: 2022-10-28

O

Originiator

Computational Framework Separating Single-Cell RNA-Seq by Genetic and Contextual Information

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"Originator: Computational Framework Separating Single-Cell RNA-Seq by Genetic and Contextual Information"
DOI: 10.1101/2024.04.04.588144, Citations: 0

Platform: R
Code: https://github.com/lanagarmire/Originator
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License: MIT
Categories: Immune, Quality Control, Variants
Added: 2024-04-12, Updated: 2025-01-30

P

ProjecTILs

Computational tool to project new scRNA-seq data into a reference map of T cells, allowing their direct comparison in a stable, annotated system of coordinates.

Publications: 1, Preprints: 1, Total citations: 337

Publications
"Interpretation of T cell states from single-cell transcriptomics data using reference atlases"
DOI: 10.1038/s41467-021-23324-4, Published: 2021-05-20, Citations: 334
Preprints
"Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses"
DOI: 10.1101/2020.06.23.166546, Citations: 3

Platform: R
Code: https://github.com/carmonalab/ProjecTILs
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License: GPL-3.0
Categories: Classification, Dimensionality Reduction, Immune, Visualisation
Added: 2020-07-03, Updated: 2020-07-03

S

scanalysis

Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data
Platform: R
Code: https://github.com/keshav-motwani/scanalysis
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License: MIT
Categories: Immune, Quality Control, Visualisation
Added: 2022-04-08, Updated: 2022-04-08

scHLAcount

scHLAcount allows you to count molecules in single-cell RNA-seq data for class I genes HLA-A, B, and C; and class II genes DPA1, DPB1, DRA1, DRB1, DQA1, and DQB1 using a personalized reference genome.

Publications: 1, Preprints: 1, Total citations: 23

Publications
"scHLAcount: allele-specific HLA expression from single-cell gene expression data"
DOI: 10.1093/bioinformatics/btaa264, Published: 2020-04-24, Citations: 23
Preprints
"scHLAcount: Allele-specific HLA expression from single-cell gene expression data"
DOI: 10.1101/750612, Citations: 0

Platform: Rust
Code: https://github.com/10XGenomics/scHLAcount
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License: MIT
Categories: Allele Specific, Haplotypes, Immune
Added: 2019-09-02, Updated: 2019-09-02

sciCSR

Single-cell inference of Class Switch Recombination

Publications: 1, Preprints: 1, Total citations: 14

Publications
"sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data"
DOI: 10.1038/s41592-023-02060-1, Published: 2023-11-06, Citations: 12
Preprints
"sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data"
DOI: 10.1101/2023.02.02.526789, Citations: 2

Platform: R/Python
Code: https://github.com/Fraternalilab/sciCSR
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License: GPL-3.0
Categories: Immune, Ordering, Visualisation
Added: 2023-02-10, Updated: 2024-01-05

scirpy

Scirpy is a scalable python-toolkit to analyze T cell receptor (TCR) repertoires from single-cell RNA sequencing (scRNA-seq) data

Publications: 1, Preprints: 1, Total citations: 124

Publications
"Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data"
DOI: 10.1093/bioinformatics/btaa611, Published: 2020-07-02, Citations: 121
Preprints
"Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data"
DOI: 10.1101/2020.04.10.035865, Citations: 3

Platform: Python
Code: https://github.com/icbi-lab/scirpy
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License: BSD-3-Clause
Categories: Immune, Visualisation
Added: 2020-04-14, Updated: 2020-04-14

scTCRseq

This project is an implementation of a pipeline for Single-cell RNAseq package for recovering TCR data in python.
Platform: Python
Code: https://github.com/ElementoLab/scTCRseq
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License: AGPL-3.0
Categories: Immune
Added: 2017-09-09, Updated: 2021-06-28

SiCR

A web application specialized for single cell repertoire analysis

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"SiCR: Web application for single-cell repertoire analysis and immune profiling"
DOI: 10.1101/2023.08.03.551897, Citations: 0

Platform: R
Categories: Immune, Interactive
Added: 2023-08-11, Updated: 2024-10-29

SignacX

Signac helps solve the cell type classification problem in single cell RNA sequencing

Publications: 1, Preprints: 1, Total citations: 10

Publications
"Cell Type Classification and Discovery across Diseases, Technologies and Tissues Reveals Conserved Gene Signatures of Immune Phenotypes"
DOI: 10.26502/jbsb.5107057, Published: 2023, Citations: 3
Preprints
"Cell type classification and discovery across diseases, technologies and tissues reveals conserved gene signatures and enables standardized single-cell readouts"
DOI: 10.1101/2021.02.01.429207, Citations: 7

Platform: R
Code: https://github.com/mathewchamberlain/SignacX
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License: GPL-3.0
Categories: Classification, Immune, Marker Genes
Added: 2021-02-05, Updated: 2024-01-05

signifinder

signifinder is an R package that collects and implements 46 expression-based signatures from cancer literature

Publications: 0, Preprints: 1, Total citations: 1

Preprints
"signifinder enables the identification of tumor cell states and cancer expression signatures in bulk, single-cell and spatial transcriptomic data"
DOI: 10.1101/2023.03.07.530940, Citations: 1

Platform: R
Code: https://github.com/CaluraLab/signifinder
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License: AGPL-3.0
Categories: Cell Cycle, Gene Sets, Immune, Visualisation
Added: 2023-03-17, Updated: 2023-03-17

Spectre

Spectre is an R package and computational toolkit that enables comprehensive end-to-end integration, exploration, and analysis of high-dimensional cytometry, imaging, or single-cell data from different batches or experiments

Publications: 1, Preprints: 1, Total citations: 115

Publications
"Integration, exploration, and analysis of high‐dimensional single‐cell cytometry data using Spectre"
DOI: 10.1002/cyto.a.24350, Published: 2021-04-26, Citations: 107
Preprints
"Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre"
DOI: 10.1101/2020.10.22.349563, Citations: 8

Platform: R
Code: https://github.com/ImmuneDynamics/Spectre
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License: MIT
Categories: Classification, Clustering, Differential Expression, Dimensionality Reduction, Expression Patterns, Immune, Integration, Marker Genes, Normalisation, Ordering, Quality Control, Rare Cells, Stem Cells
Added: 2021-11-05, Updated: 2021-11-05

STEGO-R

STEGO.R: an application to aid in scRNA-seq and scTCR-seq processing and analysis

Publications: 0, Preprints: 1, Total citations: 2

Preprints
"STEGO.R: an application to aid in scRNA-seq and scTCR-seq processing and analysis"
DOI: 10.1101/2023.09.27.559702, Citations: 2

Platform: R
Code: https://github.com/KerryAM-R/STEGO.R
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License: GPL-3.0
Categories: Immune
Added: 2023-10-20, Updated: 2023-10-20

STREAK

Performs receptor abundance estimation for single cell RNA-sequencing data using a supervised feature selection mechanism and a thresholded gene set scoring procedure

Publications: 1, Preprints: 1, Total citations: 1

Publications
"STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring"
DOI: 10.1371/journal.pcbi.1011413, Published: 2023-08-21, Citations: 1
Preprints
"STREAK: A Supervised Cell Surface Receptor Abundance Estimation Strategy for Single Cell RNA-Sequencing Data using Feature Selection and Thresholded Gene Set Scoring"
DOI: 10.1101/2022.11.10.516050, Citations: 0

Platform: R
Code: https://CRAN.R-project.org/package=STREAK
License: GPL-2.0-or-later
Categories: Immune
Added: 2022-12-09, Updated: 2024-01-05

T

TILPRED

R Package for the classification of tumor-infiltrating CD8+ lymphocytes (TILs) from single-cell RNA-seq data

Publications: 1, Preprints: 1, Total citations: 51

Publications
"Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq"
DOI: 10.1080/2162402X.2020.1737369, Published: 2020-03-12, Citations: 50
Preprints
"Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq"
DOI: 10.1101/800847, Citations: 1

Platform: R
Code: https://github.com/carmonalab/TILPRED
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License: GPL-3.0
Categories: Classification, Immune
Added: 2019-11-08, Updated: 2021-06-11

TimiGP

An R package to infer cell functional interactions and clinical values in tumor immune microenvironment through gene pairs

Publications: 1, Preprints: 1, Total citations: 2

Publications
"TimiGP: Inferring cell-cell interactions and prognostic associations in the tumor immune microenvironment through gene pairs"
DOI: 10.1016/j.xcrm.2023.101121, Published: 2023-07, Citations: 2
Preprints
"TimiGP: inferring inter-cell functional interactions and clinical values in the tumor immune microenvironment through gene pairs"
DOI: 10.1101/2022.11.17.515465, Citations: 0

Platform: R
Code: https://github.com/CSkylarL/TimiGP
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License: GPL-3.0
Categories: Gene Networks, Immune
Added: 2022-11-25, Updated: 2024-01-05

Tobiko

Detection of rearranged TCR (and BCR) chains in single cell experiments

Publications: 1, Preprints: 0, Total citations: 80

Publications
"Molecular mechanisms of lineage decisions in metabolite-specific T cells"
DOI: 10.1038/s41590-019-0465-3, Published: 2019-08-20, Citations: 80

Platform: Shell
Code: https://github.com/juugii/tobiko
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Categories: Alignment, Immune, Quality Control, Quantification, UMIs
Added: 2022-03-18, Updated: 2022-03-18

TraCeR

TraCeR - reconstruction of T cell receptor sequences from single-cell RNA-seq data.

Publications: 1, Preprints: 0, Total citations: 383

Publications
"T cell fate and clonality inference from single-cell transcriptomes"
DOI: 10.1038/nmeth.3800, Published: 2016-03-07, Citations: 383

Platform: Python
Code: https://github.com/teichlab/tracer
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License: Apache-2.0
Categories: Alignment, Assembly, Immune, Quantification, Visualisation
Added: 2016-09-08, Updated: 2017-09-11

TRAPeS

TRAPeS (TCR Reconstruction Algorithm for Paired-End Single-cell), software for reconstruction of T cell receptors (TCR) using short, paired-end single-cell RNA-sequencing.

Publications: 1, Preprints: 1, Total citations: 76

Publications
"Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state"
DOI: 10.1093/nar/gkx615, Published: 2017-07-17, Citations: 71
Preprints
"Targeted reconstruction of T cell receptor sequence from single cell RNA-sequencing links CDR3 length to T cell differentiation state"
DOI: 10.1101/072744, Citations: 5

Platform: Python
Code: https://github.com/yoseflab/trapes
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License: Custom
Categories: Immune, Quantification
Added: 2016-11-10, Updated: 2017-09-09

TRIBAL

TRIBAL is a method to infer B cell clonal lineages and isotype transition probabilities for a set of n B cells clustered into k clonotypes

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"TRIBAL: Tree Inference of B cell Clonal Lineages"
DOI: 10.1101/2023.11.27.568874, Citations: 0

Platform: Python
Code: https://github.com/elkebir-group/tribal
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License: BSD-3-Clause
Categories: Immune, Ordering, Visualisation
Added: 2023-12-01, Updated: 2024-09-15

TRUST4

Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors

Publications: 1, Preprints: 0, Total citations: 198

Publications
"TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data"
DOI: 10.1038/s41592-021-01142-2, Published: 2021-05-13, Citations: 198

Platform: C/C++
Code: https://github.com/liulab-dfci/TRUST4
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Assembly, Immune
Added: 2021-05-21, Updated: 2024-04-12

V

VDJdive

This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline
Platform: R
Code: https://github.com/kstreet13/VDJdive
starsN/A
forksN/A
last commitUnknown
License: Artistic-2.0
Categories: Immune, Integration, Visualisation
Added: 2022-11-04, Updated: 2022-11-04

VDJPuzzle

TCR and BCR reconstruction from scRNA-seq data

Publications: 1, Preprints: 1, Total citations: 90

Publications
"B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle"
DOI: 10.1093/bioinformatics/bty203, Published: 2018-04-05, Citations: 88
Preprints
"B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle"
DOI: 10.1101/181156, Citations: 2

Platform: Python/Shell
Code: https://bitbucket.org/kirbyvisp/vdjpuzzle2
License: Custom
Categories: Alignment, Assembly, Immune, Quantification, Visualisation
Added: 2017-09-01, Updated: 2018-04-17

W

WAT3R

Workflow for the Association of T-cell receptors from 3' single-cell RNA-seq

Publications: 1, Preprints: 1, Total citations: 7

Publications
"WAT3R: recovery of T-cell receptor variable regions from 3′ single-cell RNA-sequencing"
DOI: 10.1093/bioinformatics/btac382, Published: 2022-06-08, Citations: 6
Preprints
"WAT3R: Recovery of T-Cell Receptor Variable Regions From 3’ Single-Cell RNA-Sequencing"
DOI: 10.1101/2022.01.26.477886, Citations: 1

Platform: R/Python
Code: https://github.com/mainciburu/WAT3R
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Clustering, Immune, Quality Control, Quantification, Visualisation
Added: 2022-02-04, Updated: 2022-08-26

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