bioinfocz / scdrake
A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like pipeline toolkit for the R language.
☆11Updated 7 months ago
Alternatives and similar repositories for scdrake:
Users that are interested in scdrake are comparing it to the libraries listed below
- This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL☆55Updated 2 years ago
- R package for the analysis of single-cell immune repertoires☆42Updated 2 months ago
- ☆79Updated last year
- Using TCR and expression for sequence embedding☆54Updated 3 months ago
- ☆38Updated 2 months ago
- R package for Pathway RespOnsive GENe activity inference☆104Updated 2 years ago
- Unified access to several second-generation deconvolution methods☆71Updated 3 weeks ago
- ☆63Updated 10 months ago
- Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.☆90Updated 4 months ago
- COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data…☆61Updated last month
- Code related to the Celligner manuscript☆46Updated 4 years ago
- ☆57Updated 4 years ago
- Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR☆84Updated 10 months ago
- Please consider using/contributing to https://github.com/nf-core/scdownstream☆25Updated 10 months ago
- Code repository for the Tumor Immune Cell Atlas (TICA) project☆61Updated 3 years ago
- A unified interface to spatial transcriptomics deconvolution tools☆41Updated 3 weeks ago
- Framework for sensitive DE testing (using neighbourhoods)☆66Updated 9 months ago
- Coarse-graining of large single-cell RNA-seq data into metacells☆77Updated 8 months ago
- Gene group activity utility functions for Scanpy☆74Updated 4 months ago
- ☆18Updated 3 years ago
- A single cell transcriptomics pipeline for QC, integration and making the data presentable☆56Updated this week
- SciLifeLab SIB Summer School for Advanced topics in Single Cell Omics. Site: https://nbisweden.github.io/single-cell_sib_scilifelab_2021/☆23Updated 3 years ago
- Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration☆96Updated last month
- Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.☆81Updated last year
- marker-based purification of cell types from single-cell RNA-seq datasets☆110Updated last week
- Pan-Cancer Single Cell Classifier☆68Updated 11 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆60Updated 10 months ago
- ☆62Updated last year
- Inference of TCR motifs☆30Updated last week
- ☆54Updated last year