Cookie Consent by TermsFeed Generator scRNA-tools

Tools

View entries for individual tools

A

B

  • 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
    • "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
    starsN/A
    forksN/A
    last commitUnknown
  • License: Custom
  • Categories: Alignment, Immune
  • Added: 2018-08-24, Updated: 2018-08-24

C

  • Change-O is a collection of tools for processing the output of V(D)J alignment tools (e.g. IMGT/HighV-QUEST and IgBLAST), assigning clonal clusters to immunoglobulin sequences, and reconstructing germline sequences. This tool is part of the Immcantation software suite.

    • Publications
    • "Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data"
      DOI: 10.1093/bioinformatics/btv359, Published: 2015-06-10, Citations: 780
  • Platform: Python
  • Code: https://github.com/immcantation/changeo
    starsN/A
    forksN/A
    last commitUnknown
  • License: AGPL-3.0
  • Categories: Alignment, Immune
  • Added: 2025-04-12, Updated: 2025-04-12

D

E

F

G

I

M

  • 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
    • "Antigen receptor repertoire profiling from RNA-seq data"
      DOI: 10.1038/nbt.3979, Published: 2017-10-11, Citations: 268
    • "MiXCR: software for comprehensive adaptive immunity profiling"
      DOI: 10.1038/nmeth.3364, Published: 2015-04-29, Citations: 1463
  • 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

N

P

  • The REpertoire Sequencing TOolkit (pRESTO) is composed of a suite of utilities to handle all stages of raw sequence processing prior to alignment against reference germline sequences (germline segment assignment). This tool is part of the Immcantation software suite.

    • Publications
    • "pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires"
      DOI: 10.1093/bioinformatics/btu138, Published: 2014-03-10, Citations: 445
  • Platform: Python
  • Code: https://github.com/immcantation/presto
    starsN/A
    forksN/A
    last commitUnknown
  • License: AGPL-3.0
  • Categories: Alignment, Immune, UMIs
  • Added: 2025-04-12, Updated: 2025-04-12

R

  • Alignment, quantification and analysis of second and third generation sequencing data

    • Publications
    • "The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads"
      DOI: 10.1093/nar/gkz114, Published: 2019-02-20, Citations: 2368
    • Preprints
    • "The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads"
      DOI: 10.1101/377762, Citations: 50
  • Platform: R
  • License: GPL-3.0
  • Categories: Alignment, Quantification
  • Added: 2020-04-29, Updated: 2020-04-29

S

T

U

V

  • VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data.
  • Platform: Rust
  • Code: https://github.com/10XGenomics/vartrix
    starsN/A
    forksN/A
    last commitUnknown
  • License: MIT
  • Categories: Alignment, Variants
  • Added: 2018-09-14, Updated: 2018-09-14

W

Z