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Open Sustainable Technology

https://github.com/marvinquiet/cellcano

Supervised cell type identification for scATAC-seq data
bioinformatics cell-type-classification cell-type-identification celltype-annotation single-cell supervised-classification-methods
Added: over 1 year ago - Last Synced: 11 months ago - Created: January 17, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 72
  • Committers: 5
  • Issues: 10
  • Pull Requests: 4
  • Owner: marvinquiet
  • Stars: 10
  • Forks: 2
  • Packages: 1
  • Downloads: 66
https://github.com/epigen/mixscape_seurat

A Snakemake workflow for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.
bioinformatics biomedical-data-science perturbation-analysis sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 14, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 20
  • Committers: 2
  • Issues: 4
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 2
  • Forks: 0
  • Packages: 0
https://github.com/epigen/dea_seurat

A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
bioinformatics biomedical-data-science differential-expression-analysis scrna-seq single-cell snakemake snrna-seq visualization volcano-plot workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 20, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 19
  • Committers: 2
  • Issues: 10
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 10
  • Forks: 10
  • Packages: 0
https://github.com/core-bioinformatics/clustassess

Tools for assessing clustering robustness
bioinformatics clustering genomics machine-learning parameter-optimization robustness single-cell unsupervised-learning
Added: over 1 year ago - Last Synced: 11 months ago - Created: March 26, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 177
  • Committers: 4
  • Issues: 5
  • Pull Requests: 0
https://github.com/kharchenkolab/numbat

Haplotype-aware CNV analysis from single-cell RNA-seq
cancer-genomics cnv-detection lineage-tracing phylogeny single-cell single-cell-analysis single-cell-rna-seq spatial-transcriptomics
Added: over 1 year ago - Last Synced: 11 months ago - Created: May 25, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 790
  • Committers: 10
  • Issues: 162
  • Pull Requests: 10
  • Owner: kharchenkolab
  • Stars: 156
  • Forks: 22
  • Packages: 1
  • Downloads: 770
https://github.com/xinglab-ai/genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
bioinfomatics-pipeline bioinformatics bioinformatics-tool biomarker-discovery biomarkers cell-annotation classification-algorithm data-classification deep-learning genomic-data-analysis genomics genomics-visualization multi-omic-integration regression-algorithms single-cell tabular-data trajectory-inference visualization
Added: over 1 year ago - Last Synced: 11 months ago - Created: January 14, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 108
  • Committers: 6
  • Issues: 1
  • Pull Requests: 45
  • Owner: xinglab-ai
  • Stars: 11
  • Forks: 2
  • Packages: 1
  • Downloads: 178