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GitHub / sinanugur / scrna-workflow
scRNA workflow of Cellsnake
JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sinanugur%2Fscrna-workflow
Stars: 5
Forks: 0
Open Issues: 0
License: mit
Language: R
Repo Size: 1.44 MB
Dependencies:
68
Created: almost 2 years ago
Updated: 4 months ago
Last pushed: 4 months ago
Last synced: 4 months ago
Files
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Readme
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Dependencies
environment.yml
conda
- bedtools
- bioconductor-celldex
- bioconductor-clusterprofiler 4.6.0
- bioconductor-complexheatmap
- bioconductor-enhancedvolcano
- bioconductor-limma
- bioconductor-miqc
- bioconductor-org.hs.eg.db
- bioconductor-rhdf5lib
- bioconductor-scater 1.26.0
- bioconductor-singler
- bioconductor-topgo
- celltypist 1.3.0
- cmake
- cython
- docopt
- fuzzywuzzy
- geos 3.11.1
- hdf5
- kraken2
- levenshtein
- matplotlib-base <3.7
- numba >=0.56.4
- openblas 0.3.21
- pandas <=1.5.3
- pandoc 3.1.1
- pip
- plotly
- pysam >=0.16.0.1
- python
- python-kaleido
- r-base 4.2.2
- r-clustree 0.5.0
- r-curl
- r-expm
- r-fields
- r-ggalluvial
- r-ggpubr
- r-ggraph 2.1.0
- r-ggthemes
- r-hdf5r
- r-igraph 1.3.4
- r-librarian
- r-minqa
- r-monocle3
- r-nmf
- r-openxlsx
- r-optparse
- r-patchwork
- r-plotly
- r-r.utils
- r-randomcolor
- r-reticulate
- r-seurat 4.3.0
- r-spdep
- r-terra
- r-tidyseurat
- r-tidyverse
- r-v8
- r-viridis
- r-xml
- regex >=2021.4.4
- samtools
- scanpy >=1.9.1
- scipy
- snakemake >=7.22.0
- umap-learn
Dockerfile
docker
- ubuntu latest build