mhanbioinfo

mhanbioinfo's Stars

• nf-core/oncoanalyser

  A comprehensive cancer DNA/RNA analysis and reporting pipeline

  Language:Nextflow498

• hartwigmedical/hmftools

  Various algorithms for analysing genomics data

  Language:Java19658

• oicr-gsi/purple

  Language:WDL1

• KhiabanianLab/All-FIT

  All-FIT - Allele-Frequency-based Imputation of Tumor Purity

  Language:Python173

• SD-Genomics/DeviCNV

  Detection and Visualization of Exon-Level Copy Number Variants in Targeted Next Generation Sequencing Data

  Language:Python174

• BoevaLab/ONCOCNV

  ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data

  Language:R2412

• etal/cnvkit-examples

  Example datasets for CNVkit (http://github.com/etal/cnvkit)

  Language:Python195

• etal/cnvkit

  Copy number variant detection from targeted DNA sequencing

  Language:Python549166

• PeeperLab/CopywriteR

  DNA copy number detection from off-target sequence data

  Language:R3010

• FoundationMedicineInc/SGZ

  Language:Python3826

• eol017/CNV-Z

  CNV-Z is a copy number caller software for detection of copy number variation from next generation sequencing data.

  Language:Julia31

• ElsevierSoftwareX/SOFTX-D-23-00424

  CNV-Z is a copy number caller software for detection of copy number variation from next generation sequencing data.

  1

• alexdobin/STAR

  RNA-seq aligner

  Language:C1.9k506

• oicr-gsi/arriba

  Fusion caller which runs off of STAR bam

  Language:WDL2

• HTGenomeAnalysisUnit/SCE-VCF

  Sample Contamination Estimate from VCF

  Language:Nim19

• grailbio/conta

  Conta is an R package to detect cross contamination and source of contamination

  Language:R107

• jagadhesh89/MiCon

  Microhaplotype Contamination Detection workflow using Supervised learning approach

  Language:Jupyter Notebook1

• Griffan/VerifyBamID

  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

  Language:mupad9415

• AutoDarkMode/Windows-Auto-Night-Mode

  Automatically switches between the dark and light theme of Windows 10 and Windows 11

  Language:C#7.6k266

• ExpressionAnalysis/STAR-SEQR

  RNA Fusion Detection and Quantification

  Language:Python1712

• ndaniel/fusioncatcher

  Finder of Somatic Fusion Genes in RNA-seq data

  Language:Python14267

• lima1/PureCN

  Copy number calling and variant classification using targeted short read sequencing

  Language:R12732

• SimCab-CHU/ifCNV

  Language:HTML92

• ericminikel/ngs-scripts

  Scripts dealing with various aspects of next-gen sequence data. QC, CNVs, etc

  Language:R45

• vplagnol/ExomeDepth

  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

  Language:C6527

• Illumina/SpliceAI

  A deep learning-based tool to identify splice variants

  Language:Python409160

• stjude/proteinpaint

  Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.

  Language:JavaScript195

• mikessh/oncofuse

  Predicting oncogenic potential of gene fusions

  Language:Groovy124

• crazyhottommy/PRADA_pipeline_Verhaak_lab

  Language:Shell22

• GangCaoLab/CoolBox

  Jupyter notebook based genomic data visualization toolkit.

  Language:Python22737