Command-line toolkit for genomic datasets.
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Updated
Aug 20, 2019 - Haskell
Command-line toolkit for genomic datasets.
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
Experiments for evaluating SECEDO, clustering tumor cells based on single cell sequencing data
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication
Analysis of paired tumor-normal whole exome sequencing data generated in a pilot open-access study of participants in Texas.
Personalized reference editor for somatic mutation discovery
A collection of scripts documenting the parameter settings used to apply variant discovery to the exploration of Duodenal Polyposis.
A Haskell script that performs basic filtration, using a filtration string, on somatic variant data.
Empirical Bayes somatic variant calling
A Haskell script for selecting variants from a variant calling format (vcf) file based on variants present in a mgibed file.
R package containing a R Shiny app for somatic genomic variants interpretation and a tool suite to deal with an underlying local structured database.
a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
Flujos de trabajos desarrollados y automatizados en el INMEGEN para el procesamiento de datos genómicos y transcriptómicos.
A pipeline for mitochondrial mutation calling
an example open source somatic variant analysis pipeline. vLoD algorithm is also integrated.
Clustering tumor cells based on SNVs from single-cell sequencing data
Tumour-in-Normal Contamination assessment with evolutionary theory.
pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data
a Nextflow ACE-Seq calling and annotation pipeline based on DKFZ-ODCF/ACEseqWorkflow
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