CC_vel takes in single cell RNAseq data, establishes a cell cycle based pseudotime and calculates the cell cycle time derivative for each gene.

public 1yr ago 0 bookmarks

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Overview

CC_vel was developed within the BiGR group at NTNU. It takes in loom files generate

Code Snippets

shell:
    "python {params.script} 2> {log} {input} {params.barcodes} {params.mito_genes} {params.CC_genes} {output.cc_loom} {output.all_gene_loom}"

SnakeMake From line 22 of master/Snakefile

shell:
    "python {params.script} 2> {log} {input} {output.boundaries_csv} {params.num_k}"

SnakeMake From line 38 of master/Snakefile

shell:
    "python {params.script} 2> {log} {input} {params.number_of_iterations} {params.num_k}"

SnakeMake From line 60 of master/Snakefile

shell:
    "python {params.script} 2> {log} {input} {params.number_of_iterations} {params.z_CI_value} {output.merged_res}"

SnakeMake From line 80 of master/Snakefile

shell:
    "python {params.script} 2> {log} {input} {params.num_iters} {output.ranked_genes} {output.delay_genes} {output.t_test_res}"

SnakeMake From line 97 of master/Snakefile

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Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/Ylefol/CC_vel

Name: cc_vel

Version: 1

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License: MIT License

Keywords:

Data Retention time prediction Quality control report Snakemake RNA-Seq

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