AshleyLab / stmp
Sequence to Medical Phenotypes: A pipeline featuring variant annotation, prioritization, pharmacogenomics, and tools for analyzing genomic trios (mother, father, child).
☆12Updated 8 years ago
Related projects ⓘ
Alternatives and complementary repositories for stmp
- iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patient☆14Updated 2 years ago
- This is the BWA workflow used in the PanCancer project used to allign all the BAM files.☆11Updated last year
- A small repo for storing the code for making the files and html for CCRs.☆22Updated 5 years ago
- Detecting somatic mutations and predicting tumor-specific neo-antigens☆28Updated 3 years ago
- Penetrance estimates; frequency and distribution of secondary findings for the ACMG-59 gene panel☆1Updated 7 years ago
- Expectation-Maximization algorithm for Allele-Specific Expression☆21Updated last year
- This repository contains the source code of the revised version of MutPanning. MutPanning is publicly available under the BSD3-Clause ope…☆12Updated 5 years ago
- Interpretable prioritization of splice variants in diagnostic next-generation sequencing☆15Updated 6 months ago
- The official repository for the deepSNV bioconductor packages. Branch master tracks the official Bioconductor development branch.☆14Updated 2 years ago
- WDL workflow for population variant calling using htsget, DeepVariant, and GLnexus☆10Updated 6 years ago
- A comprehensive gene set function enrichment tool for multiple species.☆13Updated 4 years ago
- A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.☆28Updated 3 months ago
- A Weighted Exact Test for Mutually Exclusive Mutations in Cancer☆21Updated 6 years ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆29Updated 3 years ago
- A Feature Density Estimator for High-Throughput Sequence Tags☆23Updated 3 years ago
- Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.☆28Updated 3 years ago
- A curated list of awesome clonality and tumor heterogeneity resources☆15Updated 5 years ago
- Comprehensive Human Expressed SequenceS☆16Updated 3 months ago
- R package specialized in HLA typing clustering and visualization based on specific similarity metrics☆12Updated 5 years ago
- functions and algorithms for single cell RNA-seq analyses☆12Updated 3 years ago
- Detection of structural variants in cancer mate-pair and paired-end data☆12Updated 5 years ago
- filtering trio-based genetic variants in VCFs for clinical review☆20Updated 4 years ago
- Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding☆10Updated 3 years ago
- TSIS: an R package to infer time-series isoform switch of alternative splicing☆3Updated last year
- Fast, accurate and simple to use command line tool for variant detection in NGS data.☆10Updated 5 years ago
- Aggregation and analyses of rare CNVs across diseases☆14Updated last year
- Personal diploid genome creation and coordinate conversion☆21Updated 2 months ago
- Annotation and Prediction of Oncogenic Gene Fusions in RNAseq☆11Updated 8 years ago
- ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the hum…☆19Updated 5 years ago
- Code to reproduce analyses from the sleuth paper☆16Updated 6 years ago