{"id":18966473,"url":"https://github.com/laminetourelab/singlecell-rnaseq-tools","last_synced_at":"2025-09-05T18:31:56.678Z","repository":{"id":207570724,"uuid":"719574464","full_name":"LamineTourelab/SingleCell-rnaseq-tools","owner":"LamineTourelab","description":"This repository contains single cell analysis pipelines. 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See [scVelo](https://scvelo.readthedocs.io/en/stable/).\n\nFirst of all, the input data for scVelo are two count matrices of pre-mature (unspliced) and mature (spliced) abundances, which can be obtained from standard sequencing protocols, using the velocyto or kallisto counting pipeline. Here is velocyto example:\n\n```\nvelocyto run10x -m repeat_msk.gtf mypath/sample01 somepath/refdata-cellranger-mm10-1.2.0/genes/genes.gtf\n```\nWhere genes.gtf is the genome annotation file provided with the cellranger pipeline. repeat_msk.gtf is the repeat masker file. See [Velocyto.org](https://velocyto.org/velocyto.py/index.html).\n\n\n+ Create a conda environment with the latest  python version. Here ```3.11.5```.\n  \n``` conda create -n RNAvelocity ```\n\n+ Install the following packages versions\n  \n``` \npip install numpy==1.21.1 pandas==1.1.5 matplotlib==3.7.3 scanpy==1.9.6 igraph==0.9.8 scvelo==0.2.5 loompy==3.0.6 anndata==0.8.0\n```\nThe following packages may be needed\n\n```\npip install tqdm\npip install ipywidgets\n```\n### Cellrank using rna velocity\n\nUsing the same conda environment ```RNAvelocity```\n\nInstall cellrank with conda:\n\n```conda install -c conda-forge cellrank```\n\n## Expimap\n\nExpiMap learns to map cells into biologically understandable components representing known ‘gene programs’. The activity of each cell for a gene program is learned while simultaneously refining them and learning de novo programs.\n\n```\ngit clone https://github.com/theislab/scarches\ncd scarches\nconda env create -f envs/scarches_linux.yaml\nconda activate scarches\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flaminetourelab%2Fsinglecell-rnaseq-tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flaminetourelab%2Fsinglecell-rnaseq-tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flaminetourelab%2Fsinglecell-rnaseq-tools/lists"}