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sarek Public
Forked from nf-core/sarekAnalysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Nextflow MIT License UpdatedMay 13, 2025 -
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oncoanalyser Public
Forked from nf-core/oncoanalyserA comprehensive cancer DNA/RNA analysis and reporting pipeline
Nextflow MIT License UpdatedFeb 20, 2025 -
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long-read-pipelines Public
Forked from broadinstitute/long-read-pipelinesLong read production pipelines
Jupyter Notebook BSD 3-Clause "New" or "Revised" License UpdatedOct 3, 2024 -
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IARC-nf Public
Forked from IARCbioinfo/IARC-nfList of IARC bioinformatics nextflow pipelines
GNU General Public License v3.0 UpdatedJul 29, 2024 -
nf-casereports Public
Forked from mskilab-org/nf-gosEnd to end cancer genomics pipeline
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CASCC Public
Forked from LingyiC/CASCCCASCC: A co-expression assisted single-cell RNA-seq data clustering method
R MIT License UpdatedApr 29, 2024 -
GDD_ENS Public
Forked from mmdarmofal/GDD_ENSTumor type classifier using cancer genomic panel sequencing data
R UpdatedMar 12, 2024 -
infercna Public
Forked from jlaffy/infercnaInfer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data
R GNU General Public License v3.0 UpdatedJan 12, 2024 -
AmpliconRepository Public
Forked from AmpliconSuite/AmpliconRepositoryWebsite to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
JavaScript BSD 3-Clause "New" or "Revised" License UpdatedDec 11, 2023 -
SexInference Public
Forked from SexChrLab/SexInferenceInfer sex from DNA sequencing data and RNA sequencing data
R GNU General Public License v3.0 UpdatedDec 5, 2023 -
CycleViz Public
Forked from AmpliconSuite/CycleVizVisualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.
Python GNU General Public License v3.0 UpdatedOct 27, 2023 -
nature2023Jake-focal-amplification Public
Forked from parklab/focal-amplificationR UpdatedOct 23, 2023 -
medullo-ecdna Public
Forked from auberginekenobi/medullo-ecdnaCode accompanying Chapman et al 2021, "The landscape of extrachromosomal circular DNA in medulloblastoma"
Jupyter Notebook MIT License UpdatedOct 20, 2023 -
xTea Public
Forked from parklab/xTeaComprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
Python Other UpdatedOct 13, 2023 -
SVclone Public
Forked from mcmero/SVcloneA computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
Python BSD 3-Clause "New" or "Revised" License UpdatedAug 21, 2023 -
fingerprint_maps Public
Forked from naumanjaved/fingerprint_mapsCreate "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.
Python UpdatedMay 24, 2023 -
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platinum Public
Forked from hartwigmedical/platinumRun multiple Pipeline5 instances at once
Java GNU General Public License v3.0 UpdatedMay 2, 2023 -
circdna Public
Forked from nf-core/circdnaPipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
Python MIT License UpdatedMar 10, 2023 ecSimulator Public
Forked from AmpliconSuite/ecSimulatorSimulate ecDNA structures with user-specified properties.
Python UpdatedFeb 6, 2023 adaptiveAttractor Public
Forked from LingyiC/adaptiveAttractorThe adaptive version of attractor algorithm.
R UpdatedJan 23, 2023 ccube Public
Forked from keyuan/ccubeBayesian mixture models for estimating and clustering cancer cell fractions
R GNU General Public License v3.0 UpdatedDec 20, 2022 SigProfilerSingleSample Public
Forked from AlexandrovLab/SigProfilerSingleSampleSigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability…
Python UpdatedDec 9, 2022
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