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  • With this package .fsa intensity files or files with sequencing lengths representing the CDR3 region of T-cell receptors can be loaded, visualized and scored for quantification of the immune repertoire.
  • Platform: R
  • Code: https://github.com/martijn-cordes/ImSpectR
    starsN/A
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    last commitUnknown
  • License: MIT
  • Categories: Quantification, Visualisation
  • Added: 2019-11-08, Updated: 2019-11-08

K

  • kallisto produces transcript-level quantification estimates for RNA-seq data. It can produce transript compatibility count estimates for scRNA-seq data.

    • Publications
    • "Near-optimal probabilistic RNA-seq quantification"
      DOI: 10.1038/nbt.3519, Published: 2016-04-04, Citations: 8148
    • "Modular, efficient and constant-memory single-cell RNA-seq preprocessing"
      DOI: 10.1038/s41587-021-00870-2, Published: 2021-04-01, Citations: 334
    • "A discriminative learning approach to differential expression analysis for single-cell RNA-seq"
      DOI: 10.1038/s41592-018-0303-9, Published: 2019-01-21, Citations: 133
    • Preprints
    • "Accurate quantification of single-nucleus and single-cell RNA-seq transcripts"
      DOI: 10.1101/2022.12.02.518832, Citations: 14
    • "kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq"
      DOI: 10.1101/2023.11.21.568164, Citations: 12
    • "Identification of transcriptional signatures for cell types from single-cell RNA-Seq"
      DOI: 10.1101/258566, Citations: 11
    • "Modular and efficient pre-processing of single-cell RNA-seq"
      DOI: 10.1101/673285, Citations: 81
    • "Near-optimal RNA-Seq quantification"
      arXiv: 1505.02710, Citations: 0
  • Platform: C/C++
  • Code: https://github.com/pachterlab/kallisto
    starsN/A
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    last commitUnknown
  • License: BSD-2-Clause
  • Categories: Quantification, UMIs
  • Added: 2018-06-08, Updated: 2023-11-24

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  • 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: 2191
    • Preprints
    • "The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads"
      DOI: 10.1101/377762, Citations: 46
  • Platform: R
  • License: GPL-3.0
  • Categories: Alignment, Quantification
  • Added: 2020-04-29, Updated: 2020-04-29

S

  • Salmon produces transcript-level quantification estimates for RNA-seq data. It includes the Alevin pipeline for quantifying droplet scRNA-seq.

    • Publications
    • "Salmon provides fast and bias-aware quantification of transcript expression"
      DOI: 10.1038/nmeth.4197, Published: 2017-03-06, Citations: 9226
    • "A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification"
      DOI: 10.1093/bioinformatics/btaa450, Published: 2020-07-13, Citations: 17
    • "Alevin efficiently estimates accurate gene abundances from dscRNA-seq data"
      DOI: 10.1186/s13059-019-1670-y, Published: 2019-03-27, Citations: 216
    • Preprints
    • "Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference"
      DOI: 10.1101/021592, Citations: 98
    • "A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification"
      DOI: 10.1101/2020.04.10.035899, Citations: 0
    • "Alevin efficiently estimates accurate gene abundances from dscRNA-seq data"
      DOI: 10.1101/335000, Citations: 2
  • Platform: C++
  • Code: https://github.com/COMBINE-lab/salmon
    starsN/A
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    last commitUnknown
  • License: GPL-3.0
  • Categories: Quantification, UMIs
  • Added: 2018-06-08, Updated: 2020-04-14

T

  • 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
    • "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
    starsN/A
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    last commitUnknown
  • License: Custom
  • Categories: Immune, Quantification
  • Added: 2016-11-10, Updated: 2017-09-09

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