scRNA-tools

A

acorde

Isoform co-usage networks from single-cell RNA-seq data

Publications: 1, Preprints: 1, Total citations: 15

Publications
"acorde unravels functionally interpretable networks of isoform co-usage from single cell data"
DOI: 10.1038/s41467-022-29497-w, Published: 2022-04-05, Citations: 15
Preprints
"Acorde: unraveling functionally-interpretable networks of isoform co-usage from single cell data"
DOI: 10.1101/2021.05.07.441841, Citations: 0

Platform: R
Code: https://github.com/ConesaLab/acorde
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Alternative Splicing, Differential Expression, Visualisation
Added: 2021-05-14, Updated: 2022-04-30

airpart

Differential allelic imbalance partition across group of cells
Platform: R
Code: https://github.com/Wancen/airpart
starsN/A
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License: GPL-2.0
Categories: Alternative Splicing, Quality Control, Visualisation
Added: 2021-05-21, Updated: 2021-05-21

AltAnalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses.

Publications: 2, Preprints: 1, Total citations: 523

Publications
"Single-cell analysis of mixed-lineage states leading to a binary cell fate choice"
DOI: 10.1038/nature19348, Published: 2016-08-31, Citations: 463
"cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes"
DOI: 10.1093/nar/gkz789, Published: 2019-09-16, Citations: 57
Preprints
"cellHarmony: Cell-level matching and holistic comparison of single-cell transcriptomes"
DOI: 10.1101/412080, Citations: 3

Platform: Python
Code: https://github.com/nsalomonis/altanalyze
starsN/A
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last commitUnknown
License: Apache-2.0
Categories: Alternative Splicing, Cell Cycle, Classification, Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Networks, Gene Sets, Interactive, Marker Genes, Normalisation, Quantification, Visualisation
Added: 2017-07-16, Updated: 2018-11-12

ASTK

ASTK is a command-line software for comprehensive alternative splicing analysis

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

Publications
"ASTK: A Machine Learning‐Based Integrative Software for Alternative Splicing Analysis"
DOI: 10.1002/aisy.202300594, Published: 2024-02-07, Citations: 5
Preprints
"ASTK: a machine learning-based integrative software for alternative splicing analysis"
DOI: 10.1101/2023.01.03.522470, Citations: 0

Platform: Python/R
Code: https://github.com/huang-sh/astk
starsN/A
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License: BSD-3-Clause
Categories: Alternative Splicing, Gene Sets
Added: 2023-09-01, Updated: 2024-05-06

B

BRIE

BRIE (Bayesian regression for isoform estimate) is a Bayesian method to estimate isoform proportions from RNA-seq data.

Publications: 2, Preprints: 2, Total citations: 124

Publications
"BRIE: transcriptome-wide splicing quantification in single cells"
DOI: 10.1186/s13059-017-1248-5, Published: 2017-06-27, Citations: 92
"BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments"
DOI: 10.1186/s13059-021-02461-5, Published: 2021-08-27, Citations: 29
Preprints
"Transcriptome-wide splicing quantification in single cells"
DOI: 10.1101/098517, Citations: 1
"Computational identification of splicing phenotypes from single cell transcriptomic experiments"
DOI: 10.1101/2020.11.04.368019, Citations: 2

Platform: Python
Code: https://github.com/huangyh09/brie
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License: Apache-2.0
Categories: Alternative Splicing, Quantification
Added: 2017-01-10, Updated: 2021-09-03

D

DISCO

Distributions of Isoforms in Single Cell Omics
Platform: Python
Code: https://pbtech-vc.med.cornell.edu/git/mason-lab/disco/tree/master
Categories: Alternative Splicing
Added: 2018-03-15, Updated: 2018-03-15

DTUrtle

Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data and visualize results
Platform: R
Code: https://github.com/TobiTekath/DTUrtle
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Alternative Splicing, Visualisation
Added: 2021-06-18, Updated: 2021-06-18

F

forseti

Forseti is a predictive model to probabilistically assign a splicing status to scRNA-seq reads

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

Publications
"Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads"
DOI: 10.1093/bioinformatics/btae207, Published: 2024-06-28, Citations: 1
Preprints
"Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads"
DOI: 10.1101/2024.02.01.577813, Citations: 0

Platform: Python/R
Code: https://github.com/COMBINE-lab/forseti
starsN/A
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last commitUnknown
License: BSD-3-Clause
Categories: Alternative Splicing
Added: 2024-02-09, Updated: 2025-04-13

L

Longcell

Longcell is a package for single cell/Visium spot alternative splicing analysis

Publications: 0, Preprints: 1, Total citations: 3

Preprints
"Single cell and spatial alternative splicing analysis with long read sequencing"
DOI: 10.21203/rs.3.rs-2674892/v1, Citations: 3

Platform: R
Code: https://github.com/yuntianf/Longcell
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License: MIT
Categories: Alternative Splicing, Visualisation
Added: 2023-03-31, Updated: 2024-09-15

M

MAAPER

MAAPER is a computational method developed for model-based analysis of alternative polyadenylation using 3’ end-linked reads

Publications: 1, Preprints: 1, Total citations: 22

Publications
"MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads"
DOI: 10.1186/s13059-021-02429-5, Published: 2021-08-10, Citations: 22
Preprints
"MAAPER: model-based analysis of alternative polyadenylation using 3’ end-linked reads"
DOI: 10.1101/2021.03.21.436343, Citations: 0

Platform: R
Code: https://github.com/Vivianstats/MAAPER
starsN/A
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License: GPL-3.0
Categories: Alternative Splicing
Added: 2021-03-26, Updated: 2021-08-11

N

NOMAD

A statistical, reference-free algorithm subsumes myriad problems in genome science and enables novel discovery

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

Preprints
"Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells"
DOI: 10.1101/2022.12.06.519414, Citations: 6

Platform: Python/Nextflow/Groovy
Code: https://github.com/salzman-lab/nomad
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License: MIT
Categories: Alternative Splicing, Variants
Added: 2022-12-09, Updated: 2022-12-09

NOMAD2

NOMAD is an unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence

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

Publications
"Scalable and unsupervised discovery from raw sequencing reads using SPLASH2"
DOI: 10.1038/s41587-024-02381-2, Published: 2024-09-23, Citations: 5
Preprints
"SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads"
DOI: 10.1101/2023.03.17.533189, Citations: 7

Platform: C++/C/Python/R
Code: https://github.com/refresh-bio/NOMAD
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License: GPL-3.0
Categories: Alternative Splicing, Variants
Added: 2023-03-24, Updated: 2025-04-13

O

Outrigger

Outrigger is a program to calculate alternative splicing scores of RNA-Seq data based on junction reads and a de novo, custom annotation created with a graph database, especially made for single-cell analyses.

Publications: 1, Preprints: 0, Total citations: 169

Publications
"Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation"
DOI: 10.1016/j.molcel.2017.06.003, Published: 2017-07, Citations: 169

Platform: Python
Code: https://github.com/YeoLab/outrigger
starsN/A
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License: BSD-3-Clause
Categories: Alternative Splicing
Added: 2016-09-08, Updated: 2017-07-16

P

polyApipe

polyApipe is a pipeline for examining Alternative PolyAdenylation (APA) from 10X Genomics single-cell RNA Sequencing
Platform: Python/R
Code: https://github.com/swbioinf/polyapipe
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License: LGPL-2.1
Categories: Alternative Splicing, Quantification, UMIs
Added: 2019-07-24, Updated: 2019-07-24

Psix

Psix is a computational tool for identifying cell-state associated alternative splicing events in single cell RNA-seq (scRNA-seq) data

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

Publications
"Identifying cell state–associated alternative splicing events and their coregulation"
DOI: 10.1101/gr.276109.121, Published: 2022-07, Citations: 14
Preprints
"Identifying cell-state associated alternative splicing events and their co-regulation"
DOI: 10.1101/2021.07.23.453605, Citations: 2

Platform: Python
Code: https://github.com/lareaulab/Psix
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Categories: Alternative Splicing, Visualisation
Added: 2021-08-01, Updated: 2022-08-26

R

ReadZS

A bioinformatics best-practice analysis pipeline for The Read Z-score (ReadZS), a metric that summarizes the transcriptional state of a gene in a single cell

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

Publications
"ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq"
DOI: 10.1186/s13059-022-02795-8, Published: 2022-10-25, Citations: 10
Preprints
"ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq"
DOI: 10.1101/2021.09.29.462469, Citations: 4

Platform: Nextflow/Groovy/R/Python
Code: https://github.com/salzmanlab/ReadZS
starsN/A
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License: MIT
Categories: Alternative Splicing
Added: 2021-10-08, Updated: 2022-11-04

S

satuRn

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Publications: 1, Preprints: 1, Total citations: 24

Publications
"satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications"
DOI: 10.12688/f1000research.51749.1, Published: 2021-05-11, Citations: 20
Preprints
"satuRn: Scalable Analysis of differential Transcript Usage for bulk and single-cell RNA-sequencing applications"
DOI: 10.1101/2021.01.14.426636, Citations: 4

Platform: R
Code: https://github.com/statOmics/satuRn
starsN/A
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last commitUnknown
License: Artistic-2.0
Categories: Alternative Splicing, Visualisation
Added: 2021-01-22, Updated: 2021-05-21

SCAFE

SCAFE (Single Cell Analysis of Five-prime Ends) provides an end-to-end solution for processing of single cell 5’ end RNA-seq data

Publications: 1, Preprints: 1, Total citations: 15

Publications
"SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells"
DOI: 10.1093/bioinformatics/btac644, Published: 2022-09-29, Citations: 12
Preprints
"Profiling of transcribed cis-regulatory elements in single cells"
DOI: 10.1101/2021.04.04.438388, Citations: 3

Platform: Perl/R
Code: https://github.com/chung-lab/scafe
starsN/A
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last commitUnknown
License: MIT
Categories: Alternative Splicing, Quantification
Added: 2021-04-05, Updated: 2023-01-04

scAllele

scAllele is a versatile tool to detect and analyze nucleotide variants in scRNA-seq

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

Publications
"scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq"
DOI: 10.1126/sciadv.abn6398, Published: 2022-09-02, Citations: 7
Preprints
"scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq"
DOI: 10.1101/2022.03.29.486330, Citations: 0

Platform: Python
Code: https://github.com/gxiaolab/scAllele
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License: MIT
Categories: Alternative Splicing, Variants
Added: 2022-04-08, Updated: 2023-01-04

scAPA

This is a package and a shell script for alternative polyadenylation (APA) analysis of 3' tag single-cell RNA-seq data.

Publications: 1, Preprints: 0, Total citations: 83

Publications
"Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data"
DOI: 10.1093/nar/gkz781, Published: 2019-09-10, Citations: 83

Platform: R
Code: https://github.com/ElkonLab/scAPA
starsN/A
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License: BSD-3-Clause
Categories: Alternative Splicing
Added: 2019-09-17, Updated: 2019-09-17

scAPAtrap

Identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data

Publications: 1, Preprints: 0, Total citations: 36

Publications
"scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data"
DOI: 10.1093/bib/bbaa273, Published: 2020-11-03, Citations: 36

Platform: R
Code: https://github.com/BMILAB/scAPAtrap
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License: AGPL-3.0
Categories: Alternative Splicing, Quantification
Added: 2020-11-08, Updated: 2020-11-08

SCAPE

SCAPE is a tool for estimating alternative polyadenylation (APA) events from single-end or pair-end scRNA-seq data

Publications: 1, Preprints: 0, Total citations: 26

Publications
"SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming"
DOI: 10.1093/nar/gkac167, Published: 2022-03-14, Citations: 26

Platform: Python
Code: https://github.com/LuChenLab/SCAPE
starsN/A
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last commitUnknown
License: MIT
Categories: Alternative Splicing, Quantification
Added: 2022-03-25, Updated: 2023-08-24

SCAPE-APA

A package for estimating alternative polyadenylation events from scRNA-seq data

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

Publications
"SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data"
DOI: 10.12688/openreseurope.18673.3, Published: 2025-03-07, Citations: 0
Preprints
"SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data"
DOI: 10.1101/2024.03.12.584547, Citations: 0

Platform: Python
Code: https://github.com/chengl7-lab/scape
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last commitUnknown
License: MIT
Categories: Alternative Splicing
Added: 2024-03-22, Updated: 2025-04-13

SCAPTURE

A deep learning-embedded pipeline that captures polyadenylation information from 3 prime tag-based RNA-seq of single cells

Publications: 1, Preprints: 1, Total citations: 26

Publications
"SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells"
DOI: 10.1186/s13059-021-02437-5, Published: 2021-08-10, Citations: 25
Preprints
"SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3’ tag-based RNA-seq of single cells"
DOI: 10.1101/2021.03.17.435782, Citations: 1

Platform: Shell/Python/R
Code: https://github.com/YangLab/SCAPTURE
starsN/A
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last commitUnknown
License: Custom
Categories: Alternative Splicing, Quantification
Added: 2021-03-26, Updated: 2021-08-11

scasa

Scasa is a single cell transcript quantification tool tailored for single cell RNA-Sequencing data

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

Publications
"Isoform-level quantification for single-cell RNA sequencing"
DOI: 10.1093/bioinformatics/btab807, Published: 2021-12-02, Citations: 16

Platform: R/Perl
Code: https://github.com/eudoraleer/scasa
starsN/A
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License: GPL-3.0
Categories: Alignment, Alternative Splicing, Quantification
Added: 2021-12-10, Updated: 2021-12-10

scASfind

scASfind conducts rapid searching and returns feature-enriched cell types or cell type-specific splicing signatures, respectively

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

Publications
"Mining alternative splicing patterns in scRNA-seq data using scASfind"
DOI: 10.1186/s13059-024-03323-6, Published: 2024-07-29, Citations: 1
Preprints
"Mining alternative splicing patterns in scRNA-seq data using scASfind"
DOI: 10.1101/2023.08.19.553947, Citations: 1

Platform: R/C++
Code: https://github.com/hemberg-lab/scASfind
starsN/A
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License: MIT
Categories: Alternative Splicing, Marker Genes, Visualisation
Added: 2023-08-24, Updated: 2025-04-13

SCASL

SCASL is a strategy of cell clustering by systematically assessing the landscapes of single-cell RNA splicing

Publications: 1, Preprints: 0, Total citations: 3

Publications
"Interrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance"
DOI: 10.1038/s41467-024-46480-9, Published: 2024-03-09, Citations: 3

Platform: Python/Perl
Code: https://github.com/xryanglab/SCASL
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License: Apache-2.0
Categories: Alternative Splicing, Clustering, Visualisation
Added: 2024-03-15, Updated: 2024-03-15

SCATS

A statistical tool to detect differential alternative splicing events using single-cell RNA-seq

Publications: 1, Preprints: 1, Total citations: 22

Publications
"Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers"
DOI: 10.1371/journal.pcbi.1007925, Published: 2020-06-05, Citations: 22
Preprints
"Detecting differential alternative splicing events in scRNA-seq with or without UMIs"
DOI: 10.1101/738997, Citations: 0

Platform: Python/Perl
Code: https://github.com/huyustats/SCATS
starsN/A
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last commitUnknown
Categories: Alternative Splicing
Added: 2019-08-26, Updated: 2020-06-16

scDALI

scDALI (single-cell differential allelic imbalance) is a statistical model and analysis framework that leverages allele-specific analyses of single-cell data to decode cell-state-specific genetic regulation

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

Publications
"scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation"
DOI: 10.1186/s13059-021-02593-8, Published: 2022-01-06, Citations: 14
Preprints
"scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation"
DOI: 10.1101/2021.03.19.436142, Citations: 2

Platform: Python
Code: https://github.com/PMBio/scdali
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License: BSD-3-Clause
Categories: Alternative Splicing
Added: 2022-01-14, Updated: 2022-01-14

scDAPA

scDAPA - a tool for detection and visualization of dynamic alternative polyadenylation from scRNA-seq dataq

Publications: 1, Preprints: 0, Total citations: 27

Publications
"scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data"
DOI: 10.1093/bioinformatics/btz701, Published: 2019-09-06, Citations: 27

Platform: Shell/R
Code: https://sourceforge.net/projects/scdapa/
License: GPL-1.0
Categories: Alternative Splicing, Visualisation
Added: 2019-09-17, Updated: 2019-09-17

scDaPars

scDaPars is a bioinformatics algorithm to accurately quantify Alternative Polyadenylation (APA) events at both single-cell and single-gene resolution using standard scRNA-seq data

Publications: 1, Preprints: 1, Total citations: 42

Publications
"Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression"
DOI: 10.1101/gr.271346.120, Published: 2021-05-25, Citations: 39
Preprints
"Dynamic Analysis of Alternative Polyadenylation from Single-Cell RNA-Seq (scDaPars) Reveals Cell Subpopulations Invisible to Gene Expression Analysis"
DOI: 10.1101/2020.09.23.310649, Citations: 3

Platform: R
Code: https://github.com/YiPeng-Gao/scDaPars
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Categories: Alternative Splicing
Added: 2021-06-04, Updated: 2021-06-04

scisorseqr

scisorseqr is a linux based R-package for analyzing differential isoform expression in single cells

Publications: 1, Preprints: 1, Total citations: 163

Publications
"A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain"
DOI: 10.1038/s41467-020-20343-5, Published: 2021-01-19, Citations: 160
Preprints
"Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development"
DOI: 10.1101/2020.08.27.268730, Citations: 3

Platform: R/Shell/Awk/Python
Code: https://github.com/noush-joglekar/scisorseqr
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License: MIT
Categories: Alignment, Alternative Splicing, Quantification
Added: 2021-02-05, Updated: 2021-02-05

ScisorWiz

ScisorWiz is a linux-based R-package for visualizing differential isoform expression for any gene across any number of cell types

Publications: 1, Preprints: 1, Total citations: 19

Publications
"ScisorWiz: visualizing differential isoform expression in single-cell long-read data"
DOI: 10.1093/bioinformatics/btac340, Published: 2022-05-23, Citations: 18
Preprints
"ScisorWiz: Visualizing Differential Isoform Expression in Single-Cell Long-Read Data"
DOI: 10.1101/2022.04.14.488347, Citations: 1

Platform: R/Python
Code: https://github.com/ans4013/ScisorWiz
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License: Custom
Categories: Alternative Splicing, Visualisation
Added: 2022-05-03, Updated: 2022-06-17

scLAPA

Learning association for single-cell transcriptomics by integrating single-cell profiling of gene expression and alternative polyadenylation

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

Preprints
"Learning association for single-cell transcriptomics by integrating profiling of gene expression and alternative polyadenylation"
DOI: 10.1101/2021.01.04.425335, Citations: 1

Platform: R
Code: https://github.com/BMILAB/scLAPA
starsN/A
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Categories: Alternative Splicing, Clustering
Added: 2021-01-08, Updated: 2021-01-08

scMAPA

A model-based method to detect APA and identify cell-type-specific APA in multi-cluster setting

Publications: 1, Preprints: 1, Total citations: 3

Publications
"scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues"
DOI: 10.1093/gigascience/giac033, Published: 2022-04-30, Citations: 3
Preprints
"Cell-type-specific alternative polyadenylation (APA) genes reveal the function of dynamic APA in complex tissues"
DOI: 10.1101/2020.07.30.229096, Citations: 0

Platform: Python/R/Shell
Code: https://github.com/ybai3/scMAPA
starsN/A
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last commitUnknown
License: BSD-3-Clause
Categories: Alternative Splicing, Quantification
Added: 2022-05-06, Updated: 2022-05-06

scNanoGPS

scNanoGPS is a computational toolkit for analyzing high throughput single cell nanopore sequencing data to detect Genotypes and Phenotype Simultaneously from same cells

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

Preprints
"Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomes"
DOI: 10.1101/2023.01.24.525264, Citations: 0

Platform: Python
Code: https://github.com/gaolabtools/scNanoGPS
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last commitUnknown
License: GPL-3.0
Categories: Alignment, Alternative Splicing, Quantification, UMIs, Variants
Added: 2023-01-27, Updated: 2023-01-27

SCOTCH

Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing

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

Preprints
"Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing"
DOI: 10.1101/2024.04.29.590597, Citations: 0

Platform: R/Python
Code: https://github.com/WGLab/SCOTCH
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License: MIT
Categories: Alternative Splicing, Quantification
Added: 2024-05-06, Updated: 2024-05-06

scQuint

scQuint (single-cell quantification of introns), can perform accurate quantification, dimensionality reduction, and differential splicing analysis using short-read, full-length single-cell RNA-seq data

Publications: 1, Preprints: 1, Total citations: 15

Publications
"Robust and annotation-free analysis of alternative splicing across diverse cell types in mice"
DOI: 10.7554/elife.73520, Published: 2022-03-01, Citations: 14
Preprints
"Robust and annotation-free analysis of isoform variation using short-read scRNA-seq data"
DOI: 10.1101/2021.04.27.441683, Citations: 1

Platform: Python
Code: https://github.com/songlab-cal/scquint
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last commitUnknown
License: MIT
Categories: Alignment, Alternative Splicing, Dimensionality Reduction, Quantification
Added: 2021-04-30, Updated: 2022-03-04

SCUREL

SCUREL is a method to detect 3'UTR changes from scRNA-seq data

Publications: 1, Preprints: 1, Total citations: 9

Publications
"Shortening of 3p UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism"
DOI: 10.1261/rna.078886.121, Published: 2021-09-14, Citations: 8
Preprints
"Shortening of 3’ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism"
DOI: 10.1101/2021.06.30.450496, Citations: 1

Platform: Snakemake/Python/R
Code: https://github.com/zavolanlab/SCUREL
starsN/A
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last commitUnknown
License: Apache-2.0
Categories: Alternative Splicing, Gene Sets, Quantification, Visualisation
Added: 2021-11-05, Updated: 2021-11-05

scUTRquant

A bioinformatics pipeline for single-cell 3' UTR isoform quantification

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

Publications
"Quantifying 3′UTR length from scRNA-seq data reveals changes independent of gene expression"
DOI: 10.1038/s41467-024-48254-9, Published: 2024-05-14, Citations: 11
Preprints
"Quantification of alternative 3′UTR isoforms from single cell RNA-seq data with scUTRquant"
DOI: 10.1101/2021.11.22.469635, Citations: 5

Platform: R/Python
Code: https://github.com/Mayrlab/scUTRquant
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last commitUnknown
License: GPL-3.0
Categories: Alternative Splicing, Quantification
Added: 2021-11-27, Updated: 2025-04-13

scywalker

A program for the analysis of single cell Oxford nanopore long read data

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

Publications
"Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing"
DOI: 10.1093/bioinformatics/btae549, Published: 2024-09, Citations: 1
Preprints
"Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing"
DOI: 10.1101/2024.02.22.581508, Citations: 1

Platform: Shell
Code: https://github.com/derijkp/scywalker
starsN/A
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last commitUnknown
Categories: Alignment, Alternative Splicing, Classification, Dimensionality Reduction, Quantification, UMIs, Visualisation
Added: 2024-03-01, Updated: 2025-04-13

SiCeLoRe

SiCeLoRe (Single Cell Long Read) is a suite of tools dedicated to cell barcode / UMI assignment and bioinformatics analysis of highly multiplexed single cell Nanopore long read sequencing data.

Publications: 1, Preprints: 1, Total citations: 174

Publications
"High throughput error corrected Nanopore single cell transcriptome sequencing"
DOI: 10.1038/s41467-020-17800-6, Published: 2020-08-12, Citations: 168
Preprints
"High throughput, error corrected Nanopore single cell transcriptome sequencing"
DOI: 10.1101/831495, Citations: 6

Platform: Java
Code: https://github.com/ucagenomix/sicelore
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Allele Specific, Alternative Splicing, UMIs, Variants
Added: 2020-03-25, Updated: 2020-03-25

Sierra

Sierra is an R package designed for detecting differential transcript usage analysis from polyA-enriched single cell RNASeq data.

Publications: 1, Preprints: 1, Total citations: 79

Publications
"Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data"
DOI: 10.1186/s13059-020-02071-7, Published: 2020-07-08, Citations: 75
Preprints
"Sierra: Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data"
DOI: 10.1101/867309, Citations: 4

Platform: R
Code: https://github.com/VCCRI/Sierra
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Alternative Splicing, Visualisation
Added: 2019-12-11, Updated: 2021-06-28

SingleSplice

Algorithm for detecting alternative splicing in a population of single cells.

Publications: 1, Preprints: 0, Total citations: 56

Publications
"Robust detection of alternative splicing in a population of single cells"
DOI: 10.1093/nar/gkv1525, Published: 2016-01-05, Citations: 56

Platform: R/Perl/C++
Code: https://github.com/jw156605/SingleSplice
starsN/A
forksN/A
last commitUnknown
License: GPL-2.0
Categories: Alternative Splicing
Added: 2017-01-24, Updated: 2017-01-24

SPLASH

SPLASH is an unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence

Publications: 0, Preprints: 1, Total citations: 7

Preprints
"SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads"
DOI: 10.1101/2023.03.17.533189, Citations: 7

Platform: C++/Python/R
Code: https://github.com/refresh-bio/SPLASH
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Alternative Splicing, Quantification, Variants
Added: 2024-04-05, Updated: 2024-10-29

V

VALERIE

VALERIE enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments

Publications: 1, Preprints: 0, Total citations: 15

Publications
"VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution"
DOI: 10.1371/journal.pcbi.1008195, Published: 2020-09-08, Citations: 15

Platform: R
Code: https://github.com/wenweixiong/VALERIE
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Alternative Splicing, Visualisation
Added: 2020-09-24, Updated: 2020-09-24

velocyto

velocyto (velox + κύτος, quick cell) is a package for the analysis of expression dynamics single cell RNA seq data, in particuar it allows the estimation of the RNA velocity of single cells.

Publications: 1, Preprints: 1, Total citations: 3423

Publications
"RNA velocity of single cells"
DOI: 10.1038/s41586-018-0414-6, Published: 2018-08-08, Citations: 3392
Preprints
"RNA velocity in single cells"
DOI: 10.1101/206052, Citations: 31

Platform: Python/R
Code: https://github.com/velocyto-team/velocyto.R
starsN/A
forksN/A
last commitUnknown
Categories: Alternative Splicing, Ordering, Visualisation
Added: 2017-10-29, Updated: 2018-08-10

W

wf-single-cell

wf-single-cell is a research pipeline designed to identify the cell barcode and UMI sequences present in nanopore sequencing reads generated from single-cell gene expression libraries
Platform: Python/Nextflow/Groovy
Code: https://github.com/epi2me-labs/wf-single-cell
starsN/A
forksN/A
last commitUnknown
License: MPL-2.0
Categories: Alignment, Alternative Splicing, Dimensionality Reduction, Gene Filtering, Normalisation, Quality Control, Quantification, UMIs
Added: 2022-12-16, Updated: 2022-12-16

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