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training-material

A collection of training material from offered Galaxy courses

training-quantitative-proteomics

Training material for quantitative proteomics. Mostly R modules given in Jupyter notebooks.

transformgampoi-paper

treefar

Decision tree for analysis of RNA APA

trgated

Survival Analysis for Protein-Level TCGA Analysis

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

trtools

Toolkit for genome-wide analysis of tandem repeats

trust4

TCR and BCR assembly from RNA-seq data

trust4_analysis

tumor-immune-cell-atlas

Code repository for the Tumor Immune Cell Atlas (TICA) project

tutorials

A repository for tutorials I have linked to my website

twas-pipeline

TWAS-pipeline

tximport

Import and summarize transcript-level estimates for gene-level analysis

ucscxenashiny

📊 An R package for interactively exploring UCSC Xena https://xenabrowser.net/datapages/

umi-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

umi-tools_pipelines

Pipelines for re-analysis of iCLIP and scRNA-Seq data for UMI-tools publication

umis

Tools for processing UMI RNA-tag data | Power analysis of single-cell RNA-sequencing experiments ------------------

uplot

📈 A small, fast chart for time series, lines, areas, ohlc & bars

ursgal

Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis

usefulcode

Useful R code for functions, plotting, cool things {R}

utility_scripts

A collection of useful (mostly bash) scripts

uyar_et_al_multiomics_deeplearning

maui goes pancancer

variantstore

VariantStore: A Large-Scale Genomic Variant Search Index

variationanalysis

This repository holds the companion project to Goby3, used to train and evaluate deep learning models to call variations. This repository contains the Matcha framework to help train and evaluate deep learning models trained with semi-simulation. See docs below for details.

varlociraptor

Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.

varsim

VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications

vcf-kit

VCF-kit: Assorted utilities for the variant call format

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

vdjtools

Post-analysis of immune repertoire sequencing data

venn.js

Area proportional Venn and Euler diagrams in JavaScript