theislab / scanpy-in-R

Related projects ⓘ

Alternatives and complementary repositories for scanpy-in-R

• powellgenomicslab / DropletQC
  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
  ☆33Updated 2 years ago
• theislab / hadge
  Comprehensive pipeline for donor demultiplexing in single cell
  ☆24Updated 5 months ago
• MSingerLab / COMETSC
  COMET Single-Cell Marker Detection tool
  ☆31Updated 2 years ago
• wmacnair / psupertime
  psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
  ☆38Updated 2 years ago
• PoolLab / generecovery
  ☆29Updated last year
• kjgaulton / pipelines
  Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data
  ☆25Updated 3 years ago
• single-cell-genetics / singlecell_neuroseq_paper
  Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
  ☆21Updated 4 months ago
• single-cell-genetics / cardelino
  Clone identification from single-cell data
  ☆59Updated 2 years ago
• Mayrlab / scUTRquant
  Bioinformatics pipeline for single-cell 3' UTR isoform quantification
  ☆15Updated 5 months ago
• wenweixiong / MARVEL
  ☆40Updated 3 months ago
• davemcg / scEiaD
  Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas
  ☆24Updated 9 months ago
• lanagarmire / SSrGE
  ☆33Updated 5 years ago
• adoostparast / CellR
  CellR: single-cell RNA-Seq guided deconvolution of cellular composition from bulk-tissue RNA-Seq
  ☆15Updated 3 years ago
• netbiolab / scHumanNet
  Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3
  ☆38Updated 8 months ago
• lhe17 / nebula
  ☆28Updated 8 months ago
• shenorrLabTRDF / cellAlign
  ☆37Updated 3 years ago
• vanheeringen-lab / scepia
  Single Cell Epigenome-based Inference of Activity
  ☆19Updated last year
• mainciburu / WAT3R
  Workflow for the Association of T-cell receptors from 3' single-cell RNA-seq (WAT3R)
  ☆21Updated last year
• csoneson / rna_velocity_quant
  Evaluation of the effect of quantification choices on RNA velocity estimates
  ☆27Updated 3 years ago
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆45Updated 2 weeks ago
• broadinstitute / gtex-single-nucleus-reference
  Code repository for the snRNA-seq cross-tissue atlas project
  ☆20Updated 2 years ago
• amcdavid / CellaRepertorium
  Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
  ☆15Updated 2 years ago
• qinqian / lisa
  epigenome analysis to rank transcription factors
  ☆30Updated last year
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆42Updated last year
• jdekanter / CHETAH
  scRNA-seq cell type identification
  ☆41Updated 5 years ago
• linnarsson-lab / cytograph
  Algorithms for single-cell analysis
  ☆29Updated 3 years ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆61Updated 6 months ago
• jdime / scRNAseq_cell_cluster_labeling
  Scripts to run and benchmark scRNA-seq cell cluster labeling methods
  ☆47Updated 4 years ago
• jon-xu / scSplit
  Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples withi…
  ☆41Updated last year
• shenorrLabTRDF / bseqsc
  Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
  ☆42Updated last year