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copy-number

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broadinstitute /ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

copy-number low-coverage-sequencing cell-free-dna

UpdatedMar 20, 2024
R

lima1 /PureCN

Copy number calling and variant classification using targeted short read sequencing

copy-number bioconductor-package cell-free-dna tumor-purity tumor-heterogeneity tumor-mutational-burden loh

UpdatedMar 15, 2025
R

baudisgroup /segment-liftover

Lifterover copy number segments in whole

segment probe liftover copy-number ucsc-liftover

UpdatedFeb 6, 2024
Python

ndbrown6 /MSK-GRAIL-TECHVAL

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

r cancer ctdna copy-number cfdna clonal-hematopoiesis

UpdatedMar 27, 2020
R

gustaveroussy /EaCoN

Easy Copy Number !

r microarray segmentation copy-number exome-sequencing

UpdatedOct 18, 2021
R

polyactis /Accucopy

Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.

somatic-variants cancer-genomics expectation-maximization gaussian-mixture-models maximum-likelihood-estimation copy-number bayesian-information-criterion auto-correlation

UpdatedMar 6, 2024
C++

HenrikBengtsson /aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

package r analysis hpc notebook dna expression microarray rna reproducibility large-scale affymetrix copy-number

UpdatedMar 15, 2025
R

samabs /conliga

Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)

r genomics bayesian-methods bayesian-inference mcmc probabilistic-graphical-models copy-number-variation rcpparmadillo bayesian-nonparametric-models probabilistic-models copy-number

UpdatedOct 13, 2018
C++

HenrikBengtsson /CostelloPSCNSeq

R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data

r copy-number ht-seq

UpdatedFeb 20, 2021
R

TNTurnerLab /CNPI

Software for Rapid Analyses of Human Copy Number Data

bioinformatics genomics genome copy-number-variation genotype karyotype copy-number x-chromosome y-chromosome autosome

UpdatedFeb 5, 2025
C++

KrasnitzLab /CNprep

CNprep Package - Pre-process DNA Copy Number (CN) Data for Detection of CN Events

bootstrap r r-package copy-number-variation copy-number dna-copy-number

UpdatedMay 19, 2022
R

ndbrown6 /GAP

Genome Alteration Print (GAP)

UpdatedSep 10, 2019
R

HCL-HUBL /KILDA

KILDA (KIv2 Length Determined from a kmer Analysis) provides an alignment-free estimation of the number of KIV2 (Kringle IV type 2) repeats from FASTQ files.

bioinformatics copy-number kringle

UpdatedMar 14, 2025
Python

aleighbrown /facets_snakemake

Pipeline for running the FACETS copy number caller using Snakemake

snakemake pipeline cancer htslib facets copy-number

UpdatedMar 15, 2019
R

adeschen /CNprep

Processing DNA Copy Number (CN) Data for Detection of CN Events

bootstrap r r-package copy-number-variation copy-number model-based-clustering dna-copy-number

UpdatedMay 18, 2022
R

ndbrown6 /CNtu

Copy Number tree utilities (CNtu)

UpdatedMar 9, 2023
R

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