Alternatives and similar repositories for scRNA-codes

Users that are interested in scRNA-codes are comparing it to the libraries listed below

• XSLiuLab / tumor-immunogenicity-score
  TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020
  ☆32Updated 3 years ago
• bsml320 / scGWAS
  A method which leverages scRNA-seq data to achieve two goals: (1) to infer the cell types in which the disease-associated genes manifest …
  ☆25Updated 2 years ago
• Gibbsdavidl / Immune-Subtype-Clustering
  This repo contains the code necessary to reproduce the clusters found in "The Immune Landscape of Cancer".
  ☆18Updated 5 years ago
• ManchesterBioinference / IntegratingATAC-RNA-HiC
  scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper
  ☆24Updated 2 years ago
• xiayh17 / RNAseqStat2
  ☆16Updated 2 years ago
• quevedor2 / aneuploidy_score
  R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…
  ☆16Updated 4 years ago
• miccec / yaGST
  ☆13Updated 7 years ago
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆30Updated 2 years ago
• tgen / banovichlab
  Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).
  ☆46Updated last year
• dengchunyu / TIP
  The source code of web server TIP, including example data.
  ☆19Updated 6 years ago
• kjgaulton / pipelines
  Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data
  ☆27Updated 4 years ago
• crazyhottommy / scCustomize
  Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆16Updated 3 years ago
• saezlab / footprints
  Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"
  ☆20Updated 7 years ago
• Xiang-HF-Zhang / Dichotomous-of-innate-immune-landscape
  Dichotomous of innate immune landscape
  ☆17Updated 5 years ago
• aet21 / EpiSCORE
  Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles
  ☆33Updated 3 months ago
• gaospecial / ccgraph
  ☆11Updated 5 years ago
• bioinformatist / CrossICC
  An Interactive Consensus Clustering framework for Cross-platform data analysis
  ☆14Updated 3 years ago
• jgamache014 / snRNA-seq-workflow
  Human brain, >200,000 nuclei
  ☆24Updated 4 years ago
• junjunlab / tackPlotR
  An R package to visualize bigwigs.
  ☆31Updated 3 years ago
• UMCUGenetics / primary-met-wgs-comparison
  Code repo for all analysis done for the 'Pan-cancer whole genome comparison of primary and metastatic solid tumors' study.
  ☆16Updated 2 years ago
• Changwuuu / Cuproptosis-pancancer
  ☆18Updated last year
• foreverdream2 / dysfunction_interaction_test
  ☆29Updated 7 years ago
• TheJacksonLaboratory / BRCA-LRseq-pipeline
  Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.
  ☆16Updated 3 years ago
• junjunlab / bulkPseudotime
  Pseudotime Analysis for Bulk Data
  ☆15Updated 11 months ago
• kevlitchfield1 / CPI1000_paper
  ☆20Updated 4 years ago
• jbryois / scRNA_disease
  Code for our paper: https://www.biorxiv.org/content/10.1101/528463v1
  ☆18Updated 5 years ago
• Tuteja-Lab / TissueEnrich
  R package for tissue-specific gene enrichment
  ☆14Updated 3 years ago
• McGranahanLab / TcellExTRECT
  ☆47Updated 6 months ago
• immunogenomics / scHLApers
  Code to run the scHLApers pipeline for personalized single-cell HLA quantification
  ☆17Updated last year
• greenelab / gbm_immune_validation
  Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors
  ☆14Updated 6 years ago