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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
starsN/A
forksN/A
last commitUnknown
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

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
starsN/A
forksN/A
last commitUnknown
License: Apache-2.0
Categories: Alignment, Assembly, Immune, Quantification, Visualisation
Added: 2017-09-09, Updated: 2017-08-03

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
starsN/A
forksN/A
last commitUnknown
License: Custom
Categories: Alignment, Allele Specific, Assembly, Clustering, Immune, UMIs
Added: 2022-12-25, Updated: 2022-12-25

R

RNA-Bloom

RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler designed for scRNA-seq

Publications: 1, Preprints: 1, Total citations: 48

Publications
"RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes"
DOI: 10.1101/gr.260174.119, Published: 2020-08-17, Citations: 41
Preprints
"RNA-Bloom provides lightweight reference-free transcriptome assembly for single cells"
DOI: 10.1101/701607, Citations: 7

Platform: Java
Code: https://github.com/bcgsc/RNA-Bloom
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Assembly
Added: 2020-11-15, Updated: 2020-11-15

S

Scallop2

Scallop2 is a reference-based transcript assembler specifically optimized for paired-/multiple-end RNA-seq data

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

Publications
"Accurate assembly of multi-end RNA-seq data with Scallop2"
DOI: 10.1038/s43588-022-00216-1, Published: 2022-03-28, Citations: 14
Preprints
"Scallop2 enables accurate assembly of multiple-end RNA-seq data"
DOI: 10.1101/2021.09.03.458862, Citations: 3

Platform: C++
Code: https://github.com/Shao-Group/scallop2
starsN/A
forksN/A
last commitUnknown
License: BSD-3-Clause
Categories: Assembly
Added: 2022-04-01, Updated: 2022-04-01

scRNAss

scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions

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

Publications
"scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions"
DOI: 10.1093/bioinformatics/btz240, Published: 2019-04-05, Citations: 8

Platform: C++
Code: https://sourceforge.net/projects/single-cell-rna-seq-assembly/
License: GPL-3.0
Categories: Assembly
Added: 2019-04-16, Updated: 2019-04-16

T

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
starsN/A
forksN/A
last commitUnknown
License: Apache-2.0
Categories: Alignment, Assembly, Immune, Quantification, Visualisation
Added: 2016-09-08, Updated: 2017-09-11

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

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