Alternatives and similar repositories for self-study

Users that are interested in self-study are comparing it to the libraries listed below

• Gibbsdavidl / Immune-Subtype-Clustering
  This repo contains the code necessary to reproduce the clusters found in "The Immune Landscape of Cancer".
  ☆18Updated 6 years ago
• jokergoo / ComplexHeatmap_v2_paper_code
  ☆20Updated 3 years ago
• zdq0808 / TMEscore
  Calculating Tumor microenvironment score
  ☆29Updated 2 years ago
• XSLiuLab / tumor-immunogenicity-score
  TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020
  ☆33Updated 4 years ago
• xjsun1221 / RSEM_with_limma_edgeR_Deseq2
  ☆37Updated 5 years ago
• songw01 / MEGENA
  Multiscale embedded gene co-expression network analysis
  ☆56Updated last year
• youqiongye / HAMFA
  Hypoxia associated molecular feature analysis
  ☆36Updated 6 years ago
• kerseviciute / aPEAR
  Enrichment Networks for Pathway Enrichment Analysis
  ☆63Updated 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
• icbi-lab / Immunophenogram
  ☆41Updated 7 years ago
• junjunlab / bulkPseudotime
  Pseudotime Analysis for Bulk Data
  ☆18Updated last year
• YuLab-SMU / tigeR
  🐯 tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package
  ☆35Updated 6 months ago
• zdq0808 / Blasso
  Integrating LASSO and bootstrapping algorithm to find best prognostic or predictive biomarkers
  ☆21Updated 3 years ago
• bei-lab / scRNA-of-NPC
  Tumour Heterogeneity and Intercellular Networks of Nasopharyngeal Carcinoma at Single Cell Resolution
  ☆13Updated 2 years ago
• bioinformatist / CrossICC
  An Interactive Consensus Clustering framework for Cross-platform data analysis
  ☆14Updated 3 years ago
• junjunlab / tackPlotR
  An R package to visualize bigwigs.
  ☆32Updated 3 years ago
• kevlitchfield1 / CPI1000_paper
  ☆20Updated 4 years ago
• miccec / yaGST
  ☆13Updated 8 years ago
• McGranahanLab / TcellExTRECT
  ☆48Updated 11 months ago
• ShixiangWang / gcap
  GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data a…
  ☆20Updated 3 months ago
• dengchunyu / TIP
  The source code of web server TIP, including example data.
  ☆20Updated 6 years ago
• noriakis / CBNplot
  Bayesian network plot for the enrichment analysis results
  ☆66Updated last year
• aertslab / SCopeLoomR
  R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters an…
  ☆45Updated 3 years ago
• liulab-dfci / TIDEpy
  TIDE (Tumor Immune Dysfunction and Exclusion), a gene expression biomarker to predict the clinical response to immune checkpoint blockade…
  ☆32Updated 5 years ago
• peterawe / CMScaller
  ☆32Updated 5 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.
  ☆18Updated 2 years ago
• foreverdream2 / dysfunction_interaction_test
  ☆30Updated 7 years ago
• jmzeng1314 / mouse-xx-xy-C1
  ☆18Updated 6 years ago
• GangLiLab / genekitr
  🧬 Gene analysis toolkit based on R
  ☆60Updated 11 months ago
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year