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 5 years ago
• DongqiangZeng0808 / TMEscore
  Calculating Tumor microenvironment score
  ☆29Updated 2 years ago
• kerseviciute / aPEAR
  Enrichment Networks for Pathway Enrichment Analysis
  ☆55Updated 2 years ago
• youqiongye / HAMFA
  Hypoxia associated molecular feature analysis
  ☆35Updated 5 years ago
• kevlitchfield1 / CPI1000_paper
  ☆20Updated 4 years ago
• jokergoo / ComplexHeatmap_v2_paper_code
  ☆20Updated 3 years ago
• YuLab-SMU / tigeR
  🐯 tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package
  ☆33Updated last month
• noriakis / CBNplot
  Bayesian network plot for the enrichment analysis results
  ☆64Updated 9 months 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
• Precancer / SCC
  Immune evasion before tumor invasion in early squamous lung cell carcinogenesis
  ☆16Updated 3 years ago
• bei-lab / scRNA-of-NPC
  Tumour Heterogeneity and Intercellular Networks of Nasopharyngeal Carcinoma at Single Cell Resolution
  ☆13Updated 2 years ago
• jokergoo / GSEAtopics
  ☆23Updated last month
• xjsun1221 / RSEM_with_limma_edgeR_Deseq2
  ☆37Updated 5 years ago
• icbi-lab / Immunophenogram
  ☆40Updated 7 years ago
• liulab-dfci / TIDEpy
  TIDE (Tumor Immune Dysfunction and Exclusion), a gene expression biomarker to predict the clinical response to immune checkpoint blockade…
  ☆30Updated 5 years ago
• GerkeLab / TCGAhrd
  Homologous recombination deficiency in TCGA PanCancer Atlas
  ☆27Updated 4 years ago
• miccec / yaGST
  ☆13Updated 7 years ago
• junjunlab / bulkPseudotime
  Pseudotime Analysis for Bulk Data
  ☆15Updated 11 months ago
• XSLiuLab / tumor-immunogenicity-score
  TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020
  ☆32Updated 3 years ago
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• McGranahanLab / TcellExTRECT
  ☆47Updated 6 months ago
• Zaoqu-Liu / BioEnricher
  Integrate Analysis and Visualization for Bioinformatic Enrichment Analyzer
  ☆78Updated last year
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• 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…
  ☆42Updated 3 years ago
• songw01 / MEGENA
  Multiscale embedded gene co-expression network analysis
  ☆54Updated last year
• liulab-dfci / RIMA_pipeline
  ☆82Updated last year
• junjunlab / tackPlotR
  An R package to visualize bigwigs.
  ☆31Updated 3 years ago
• BioinformaticsFMRP / PanCanStem_Web
  ☆31Updated 3 years ago
• Moonerss / CIBERSORT
  ☆39Updated 11 months ago
• foreverdream2 / dysfunction_interaction_test
  ☆29Updated 7 years ago