bahlolab / bioinfotoolsLinks
Documenting usage and experience with bioinformatic tools
☆40Updated 10 years ago
Alternatives and similar repositories for bioinfotools
Users that are interested in bioinfotools are comparing it to the libraries listed below
Sorting:
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆56Updated 5 years ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆55Updated 4 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆98Updated 3 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆77Updated 5 years ago
- R package for inferring copy number from read depth☆32Updated 2 years ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 6 years ago
- ☆69Updated 3 years ago
- Relevant papers for CNV and SV approaches☆93Updated 10 months ago
- ☆78Updated 11 years ago
- ☆57Updated 5 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆47Updated 7 years ago
- csf fork of fastqc for usage on selected reads of unaligned bam file☆48Updated 12 years ago
- phasing and Allele Specific Expression from RNA-seq☆116Updated last year
- ☆89Updated 4 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- identifying mutational significance in cancer genomes☆61Updated 2 years ago
- FEELnc : FlExible Extraction of LncRNA☆90Updated last month
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆72Updated 4 years ago
- CNV screening and annotation tool☆25Updated 8 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago
- Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline☆57Updated 5 years ago
- piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School☆60Updated 2 months ago
- A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets☆83Updated 2 years ago
- Tools for analyzing DNA methylation data☆43Updated this week
- Tip and tricks for BAM files☆86Updated 7 years ago
- Software program for checking sample matching for NGS data☆134Updated last year
- This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…☆60Updated 5 years ago
- xHLA: Fast and accurate HLA typing from short read sequence data☆113Updated last year
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆57Updated 4 years ago
- QDNAseq package for Bioconductor☆51Updated last year