R-universe search: topic:copy-number-variation

Showing 6 of total 6 results (show query)

bioc

TitanCNA:Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.

Maintained by Gavin Ha. Last updated 5 months ago.

sequencing wholegenome dnaseq exomeseq statisticalmethod copynumbervariation hiddenmarkovmodel genetics genomicvariation immunooncology 10x-genomics copy-number-variation genome-sequencing hmm tumor-heterogeneity

97 stars 8.47 score 68 scripts

bioc

CopyNumberPlots:Create Copy-Number Plots using karyoploteR functionality

CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.

Maintained by Bernat Gel. Last updated 5 months ago.

visualization copynumbervariation coverage onechannel dataimport sequencing dnaseq bioconductor bioconductor-package bioinformatics copy-number-variation genomics genomics-visualization

6 stars 6.24 score 16 scripts 2 dependents

bioc

CNVMetrics:Copy Number Variant Metrics

The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics.

Maintained by Astrid Deschênes. Last updated 5 months ago.

biologicalquestion software copynumbervariation cnv copy-number-variation metrics r-language

4 stars 5.08 score 8 scripts

seborinos

NCutYX:Clustering of Omics Data of Multiple Types with a Multilayer Network Representation

Omics data come in different forms: gene expression, methylation, copy number, protein measurements and more. 'NCutYX' allows clustering of variables, of samples, and both variables and samples (biclustering), while incorporating the dependencies across multiple types of Omics data. (SJ Teran Hidalgo et al (2017), <doi:10.1186/s12864-017-3990-1>).

Maintained by Sebastian J. Teran Hidalgo. Last updated 7 years ago.

c-plus-plus cancer-genomics clustering copy-number-variation devtools gene-expression graph-algorithms graph-cut graphs proteins rcpp cpp

4 stars 4.48 score 15 scripts

piyalkarum

rCNV:Detect Copy Number Variants from SNPs Data

Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).

Maintained by Piyal Karunarathne. Last updated 28 days ago.

cnv-analysis copy-number-variation gene-duplication genetics genomics landscape-genetics snps cpp

6 stars 4.26 score 4 scripts

shixiangwang

DoAbsolute:Automate Absolute Copy Number Calling

Provide an easy interface to automate estimation of absolute copy number, purity, ploidy using 'ABSOLUTE'.

Maintained by Shixiang Wang. Last updated 1 years ago.

absolute copy-number-variation firehose

40 stars 3.30 score 7 scripts