nf-core / scdownstreamLinks
A single cell transcriptomics pipeline for QC, integration and making the data presentable
☆69Updated this week
Alternatives and similar repositories for scdownstream
Users that are interested in scdownstream are comparing it to the libraries listed below
Sorting:
- A repository of pipelines for single-cell data in Nextflow DSL2☆75Updated 2 years ago
- ☆62Updated last year
- Tools for working with BUS files☆100Updated last month
- ☆57Updated 4 years ago
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…☆65Updated this week
- 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
- Genomic coordinates of problematic genomic regions as GRanges☆40Updated 7 months ago
- ☆82Updated last year
- UniverSC: a flexible cross-platform single-cell data processing pipeline☆45Updated last year
- Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)☆75Updated last year
- R implementation of MULTI-seq sample classification workflow☆63Updated last year
- A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.☆102Updated 2 years ago
- SNV calling from single cell sequencing☆104Updated 8 months ago
- Links to ATAC-seq analysis tools☆68Updated 3 years ago
- An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)☆115Updated 5 months ago
- Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent gen…☆32Updated 4 years ago
- Scripts to import your FeatureCounts output into DEXSeq☆33Updated 6 years ago
- A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic …☆61Updated last month
- Basic workflow for ATAC-seq analysis☆81Updated last year
- My youtube programming scripts☆54Updated 5 months ago
- Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods☆95Updated 2 years ago
- ☆40Updated this week
- Pipeline for processing inDrops sequencing data☆76Updated 6 years ago
- rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis☆54Updated last month
- A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data☆76Updated 4 months ago
- machine-readable file format for genomic library sequence and structure☆120Updated this week
- dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data☆117Updated this week
- Integrative pathway enrichment analysis of multivariate omics data☆112Updated 2 weeks ago
- RiboPlotR package for Ribo-plot☆15Updated last month
- A tool that allows to get UMI counts from a single cell protein assay☆82Updated 2 months ago