Alternatives and similar repositories for scquint:

Users that are interested in scquint are comparing it to the libraries listed below

• ConesaLab / acorde
  Isoform co-usage networks from single-cell RNA-seq data
  ☆16Updated last year
• bodegalab / irescue
  Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq
  ☆17Updated 3 weeks ago
• ans4013 / ScisorWiz
  ScisorWiz: Differential Isoform Visualizer for Long-Read RNA Sequencing Data
  ☆16Updated 11 months ago
• wenweixiong / MARVEL
  ☆49Updated 8 months ago
• caleblareau / mitoblacklist
  Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome
  ☆19Updated 2 years ago
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated last year
• hemberg-lab / MicroExonator
  Snakemake pipeline for microexon discovery and quantification
  ☆20Updated 3 months ago
• PoolLab / ReferenceEnhancer
  ☆20Updated last year
• juliaolivieri / SpliZ_pipeline
  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis
  ☆32Updated 3 years ago
• eudoraleer / scasa
  SCASA: Single cell transcript quantification tool
  ☆21Updated last year
• jacobhepkema / scover
  scover
  ☆23Updated last year
• theislab / hadge
  Comprehensive pipeline for donor demultiplexing in single cell
  ☆24Updated 10 months ago
• lareaulab / psix
  ☆16Updated last year
• qqwang-berkeley / JUM
  A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
  ☆28Updated 2 years ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago
• landau-lab / ONT-sc-splice
  Tools for detecting alternative splicing events and genotype in single-cell gene expression data.
  ☆14Updated last year
• GreenleafLab / ChrAccR
  Analyzing chromatin accessibility data in R
  ☆18Updated last year
• TheJacksonLaboratory / BRCA-LRseq-pipeline
  Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.
  ☆14Updated 2 years ago
• csoneson / rna_velocity_quant
  Evaluation of the effect of quantification choices on RNA velocity estimates
  ☆27Updated 3 years ago
• JSB-UCLA / Clipper
  A p-value-free method for controlling false discovery rates in high-throughput biological data with two conditions
  ☆39Updated 2 years ago
• salzman-lab / SICILIAN
  ☆21Updated 10 months ago
• mehdiborji / nanoranger
  simplified cellranger for long-read data
  ☆18Updated last week
• Papatheodorou-Group / CATD_snakemake
  Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq dat…
  ☆15Updated 8 months ago
• aertslab / PUMATAC
  Pipeline for Universal Mapping of ATAC-seq
  ☆25Updated 11 months ago
• zhongw2 / GeneTEFlow
  ☆23Updated 3 years ago
• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆36Updated 3 weeks ago
• icbi-lab / NeoFuse
  NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.
  ☆19Updated 2 years ago
• bedapub / splicekit
  splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
  ☆16Updated last month
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆19Updated last year