bhklab / genefu
R package providing various functions relevant for gene expression analysis with emphasis on breast cancer.
☆25Updated last month
Alternatives and similar repositories for genefu:
Users that are interested in genefu are comparing it to the libraries listed below
- ☆40Updated 6 years ago
- This repo contains the code necessary to reproduce the clusters found in "The Immune Landscape of Cancer".☆19Updated 5 years ago
- Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for man…☆51Updated 6 years ago
- ☆55Updated 2 years ago
- Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://…☆42Updated 4 years ago
- Transcriptomic tools to classify bladder tumours according to six published molecular classifications : Baylor, UNC, MDA, Lund, CIT-Curie…☆25Updated 2 years ago
- ☆34Updated 8 years ago
- Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours☆26Updated 4 years ago
- Analysis examples based on the ISB-CGC hosted TCGA data, using R and R Markdown.☆31Updated 7 years ago
- ConsensusTME Gene Sets and R Script☆39Updated 7 months ago
- Reference transcriptome indices build from kallisto for popular organisms☆41Updated last year
- ☆60Updated 4 years ago
- This repostory contains codes for Shimada et al., "A tool for browsing the Cancer Dependency Map reveals functional connections between g…☆13Updated 3 years ago
- Single-Cell Sequencing Quality Control and Processing Software☆30Updated 5 years ago
- Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hi…☆26Updated 2 years ago
- TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages☆42Updated last year
- An R client for broads firehose pipeline, providing TCGA data sets☆60Updated 5 years ago
- CONICS: COpy-Number analysis In single-Cell RNA-Sequencing☆74Updated last year
- Explore the cancer relevance of your gene list☆49Updated 4 months ago
- ☆29Updated 6 years ago
- Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline☆43Updated last year
- Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.☆24Updated 3 years ago
- Adaptive Daisy Model to discriminate core-fitness/context-specific essential genes in large scale CRISPR-Cas9 screens☆22Updated 5 years ago
- 10x single cell RNA-seq data from the developing mouse retina☆16Updated 3 years ago
- Filtering of PDX samples for mouse derived reads☆27Updated 2 years ago
- Figure depicting the breadth of multimodal scRNA-seq technologies☆15Updated 5 years ago
- Pipeline for characterizing metebolic heterogeneity from single-cell RNA-seq data☆23Updated 3 years ago
- Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem☆29Updated 6 years ago
- Processing of single cell RNAseq data for the recovery of TCRs in python☆26Updated 4 years ago
- Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"☆53Updated 3 years ago