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copynumber

Here are 9 public repositories matching this topic...

AntonioDeFalco / SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

scrna-seq single-cell copy-number-variation copynumber tumor-evolution tumor-heterogeneity aneuploidy scrna-seq-analysis subclone-identification tumor-classification clonal-evolution scrna-pipeline subclonal-deconvolution microenvironment clonal-analysis

Updated Jun 11, 2024
HTML

CompEpigen / ezASCAT

Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R

genomics ascat copynumber

Updated Dec 6, 2021
R

AmpliconSuite / AmpliconArchitect

Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.

bioinformatics cancer copynumber ecdna

Updated Sep 23, 2024
Python

PoisonAlien / varscan_accessories

accessory scripts for processing varscan somatic/copynumber outputs.

somatic-variants vcf segmentation varscan copynumber converts-varscan-somatic

Updated Dec 8, 2017
Python

Bioconductor / RaggedExperiment

Matrix-like representations of mutation and CN data

data-structure mutations copynumber core-package

Updated Oct 29, 2024
R

genepattern / AmpliconSuite

Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.

bioinformatics cancer copynumber genepattern-module ecdna

Updated Oct 24, 2024
Python

ICBI / CINdex

CINdex Bioconductor package. Read more here: https://www.bioconductor.org/packages/release/bioc/html/CINdex.html

r copynumber bioconductor-package chromsome-instability

Updated Feb 27, 2021
R

xwang234 / copynumber

Updated Apr 20, 2017
R

sebastian-gregoricchio / SPACCa

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

somatic-variants mutation gatk mutations chip-seq somatic-mutations normalization mutation-analysis copynumber macs chip-seq-callers macs2 chipseq somatic-indels gatk4 chip-seq-data chip-seq-analysis chip-seq-peaks somatic-variant

Updated Oct 18, 2024
Python

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