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tgen

tgpipeline

Pipeline for Target Sequencing Data Analysis

the-art-of-data-science

An interactive online reading of Matsui and Peng's The Art of Data Science

thermorawfileparser

Thermo RAW file parser that runs on Linux with mono

threedrnaseq

A shiny App for differential expression and differential alternative splicing analysis

thw_python_plotting

Tutorial on plotting in Python

tidy-text-mining

Manuscript of the book "Tidy Text Mining with R" by Julia Silge and David Robinson

tidygraph

A tidy API for graph manipulation

tidyverse

Easily install and load packages from the tidyverse

tissue_classification

toil-rnaseq

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline

toil-scripts

Toil workflows for common genomic pipelines

tools

tools-1

repository of open source tools developed by the ruggles lab

tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community

tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

topgo_shiny_dashboard

Web Interface for topGO and SPIA R Packages. Utilizes R shiny and shiny dashboard.

tophat

Spliced read mapper for RNA-Seq

tpot

A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.

trainflag

A flagging and questionnaire application for use during training sessions

training-material

A collection of Galaxy-related training material

training-modules

Materials for short, half-day workshops

training_fusion

Training: how to detect fusion trascript

trainingphylointro

Practical exercises and slides for my computational molecular evolution teaching

transvar

TransVar - multiway annotator for precision medicine

trim_isoseq_polya

Program to trim polyA tails

trimgalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

trinity_ctat

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

trove

Visualization and analysis of cancer hallmarks on signaling networks