exome-sequencing

There are 0 repository under exome-sequencing topic.

• gustaveroussy / EaCoN

  Easy Copy Number !

  rcopy-numbermicroarrayexome-sequencingsegmentation
  Language:R 20

• tjbencomo / ngs-pipeline

  Pipeline for Somatic Variant Calling with WES and WGS data

  snakemakebioinformaticssomatic-variantsexome-sequencing
  Language:Python 17

• nf-core / exoseq

  Please consider using/contributing to https://github.com/nf-core/sarek

  exomeexome-sequencinggenomicsnextflownf-corevariant-callingworkflow
  Language:Nextflow 15

• cibiobcg / EthSEQ

  Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data

  ethnicity-analysisexome-sequencinggenotype-data
  Language:R 11

• matheuscburger / Excavator2

  A fork of the project Excavator2 from sourceforge.

  cnvbioinformaticsexome-sequencing
  Language:R 9

• SciLifeLab / NGI-ExoSeq

  This pipeline has moved! Please see:

  bioinformatics-analysisbioinformatics-pipelineexome-pipelineexome-sequencingnextflow
  Language:Groovy 8

• cliu32 / athlates

  exome-sequencingprotocolampliconsillumina-platform
  Language:Perl 5

• KrasnitzLab / RAIDS

  Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

  ancestryinferencegenomicsr-languager-packagewhole-genome-sequencingrna-sequencingrna-seqexome-sequencingcancer-genomics
  Language:R 5

• marislab / create-pptc-pdx-oncoprints

  As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of these models is required to enable PPTC investigators to develop robust "responder hypotheses" when drug activity is observed. With funding provided by Alex's Lemonade Stand Foundation, we genomically characterize a major subset of 286 PDX models. We use whole exome sequencing, transcriptome sequencing, and SNPArray to characterize the tumor models. The focus on DNA and RNA sequencing data mirrors the current standard practice in most clinical diagnostics lab that use these technologies to detect the spectrum of targetable mutations, gene amplifications, and gene fusion events relevant to preclinical drug development.

  exome-sequencingrna-sequencingmutational-signaturesclassifierethnicity-analysisfusionclustering
  Language:R 3

• mframpton / transplot

  The transplot package can be used to make multi-track plots of Next Generation Sequencing (NGS) data for gene transcripts, namely for depth of coverage and for the distribution of variants and protein domains.

  exome-sequencingvisualizationnext-generation-sequencingdnagenetic-variantsproteinscoverage
  Language:Python 3

• sdhutchins / vcf-prepping

  Scripts used on a cluster that demonstrate vcf file manipulation and preparation.

  vcfbcftoolswhole-genome-sequencingwgsexome-sequencing
  Language:Shell 3

• manojmw / MultiOmics-ExomeSeq-Phenotype

  Main Repository for my MASTER'S THESIS PROJECT

  multiomicsinteractomeexome-sequencingphenotypemachine-learningclusteringcandidate-genesvariantsmendelianmonogenic
  Language:Python 2

• bioinf / afpaper

  Scripts and data processing notes for Russian exome sequencing AF paper

  allele-frequencieswhole-exome-sequencingrussian-specificexome-sequencing
  Language:R 1

• BU-ISCIII / exome_pipeline

  Miscellaneous pipelines for genomics computation analysis in a SGE HPC platform.

  bashexome-sequencinggatksgevariant-callingwes
  Language:Shell 1

• gari3008ma / RNA-seq

  colorectal cancer

  rna-seqgenecolon-cancercancerpathwayscrc-developmentdiseaseexome-sequencingbiomedical-engineering
  1

• pasted / variant_parser

  Selects possible pathogenic variants from an Alamut output

  variantshpovariant-parserexome-sequencing
  Language:Ruby 1

• jiatuya / SNV_prediction_model

  Note: This is a detailed Intro to this project. A brief users guide can be found at users_guide.md

  machine-learningexome-sequencingsnv
  Language:Jupyter Notebook 0

• leahkemp / hyperparathyroid_analysis_20221102

  Analysis documentation for research into the variants associated with hyperparathyroidism. Illumina, germline, human, whole exome sequence (WES) data from the CCDHB.

  clinical-researchexome-sequencingilluminawhole-exome-sequencing
  Language:Shell 0

• LuciaNhuNguyen / Masterarbeit

  Leveraging WES short reads for PAN-EXOME creation and analysis.

  exomeexome-pipelineexome-sequencingngsngs-analysisngs-pipelinepangenomepangenome-graphpangenome-pipelinepangenomic-analysis
  Language:WDL 0

• Grelot / diabetesGenetics--COAT

  COverage Analysis Tool have been developed in 2016. It aims to automatically find bad quality regions of coding sequences in a set of sequencing data. It includes a graphical interface.

  bam-filescoding-regionsexome-sequencingpythongenomegeneticsbioinformaticssamtoolsgraphical-interfaceexomesequencingngsqtgui
  Language:Python

• pasted / trio_generator

  Example workflow to generate a trio VCF from parental data

  geneticsbioinformaticsexome-sequencing
  Language:Ruby

• rivas-lab / ibd-exomes

  All QC, annotation, and analyses for IBD exomes

  crohns-diseaseexome-sequencinggeneticsinflammatory-bowel-diseaseulcerative-colitis
  Language:Jupyter Notebook