Tim Triche, Jr.

Login: ttriche

Company: Van Andel Research Institute

Location: Grand Rapids, Michigan

Bio: Statistician, #researchparasite, designer of experiments

Blog:

Blog:

Member of

2. Global Alliance for Genomics and Health
3. useR! 2014

Repositories

abyss

:microscope: De novo genome sequence assembler to assemble large genomes using short reads

aDockerFile

for anthony

api-client-r

Provides a simple R script that transforms API query results into GAlignments.

artemisData

processed HDF5 files for artemis examples

ATACseeker

ATACseq tools for Bioconductor

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

banreg

toy statistical analysis of Americans killed, by "vetting" status for country of killer's citizenship (counts subject to change)

bayesCC

Bayesian Consensus Clustering, packaged up from code by Eric F. Lock

BayesianScreening

R package to perform Bayesian screening for genomic data

BCPeakR

Xing et al's BayesianChangePoint peak caller. Currently requires patching to install as an R package.

bed

Bayesian Epiallele Detection (BED)

bigquery-examples

Example BigQuery integrations. Includes both sql and R wrappers.

bioc2015multiomicsworkshop

Challenges and opportunities from integrative analysis of multi-omic data sets

biocMultiQc2015

go directly to https://github.com/ttriche/biocMultiQc2015/blob/master/vignettes/multiAssay.Rmd

biocMultiSciDB

a proof of concept for stuffing SciDB-backended summarized experiments into a joint container

BiocParallel

Bioconductor facilities for parallel evaluation (experimental)

bioinformatics

Tools for bioinformatics

biscuitEater

a small package of bsseq tools for Biscuit output

bitstarter

null

bwa-meth

align BS-Seq reads and extract methylation without intermediate temp files

Canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.

cbioportal

cBioPortal for Cancer Genomics

chRomHMM

This WAS the repository for the ChromHMM R wrapper, which is now called 'chromophobe'.

chromophobe

a package to handle ChromHMM (http://compbio.mit.edu/ChromHMM/) and similar segmentation models in R

cometExactTest

Forked from read-only CRAN mirror to add docs, helper function, to finish up TARGET AML

COMETgazer

COMETgazer mehylation analysis software suite

conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays -

corrr

Correlations in R

D3BioFabric

JavaScript/D3 Version

d3r

d3.js helpers for R

DataFrames.jl

library for working with tabular data in Julia

datasci_course_materials

Public repository for course materials for the Data Science at Scale Specialization at Coursera

DCGAN-tensorflow

A tensorflow implementation of Deep Convolutional Generative Adversarial Networks

ddpcr

Analysis and visualization of Droplet Digital PCR data in R and on the web

dendRix

port of Dendrix (Vandin, Upfal, & Raphael, Genome Res 2011) to R

derfinder

Fast differential expression analysis of RNA-seq data at base-pair resolution

dma

Dynamic model averaging (development repo)

DMRcateExtras

devel git for DMRcate

dotfiles

dot files that I'd like not to misplace

Dropout.jl

Fast dropout training (regularization via feature corruption) for GLMs for Julia

dsub

Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.

EnsDb.Hsapiens.v80

mirror of BioC ensDb package

ensembldb

null

EpiDISH

This package contains a reference-based function to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.

FirebrowseR

An R client for broads firehose pipeline, providing TCGA data sets

fussingAboutSEs

like it says on the tin

gamlr

The gamlr package for R.

genomation

R package for genomic feature analysis and visualization

GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.

GenomicFileViews

Views across multiple files

ggBrain

Helper functions for making brain image figures with ggplot

git-and-github-cheat-sheet

Some very basic git and GitHub commands and resources.

GLM.jl

Generalized linear models in Julia

groupedPMA

new penalties for PMA (supervised/multiple CCA)

guesstimate-app

Create Fermi Estimates and Perform Monte Carlo Estimates

IGV

An R package providing interactive connections to igv.js (the Integrative Genomics Viewer) in a web browser

infiniumSnps

Illumina Infinium HumanMethylation450 and HumanMethylationEPIC SNP probe genotypes

InteractionSet

Bioconductor class for genomic interaction data

jstat

JavaScript Statistical Library

kallisto

Near-optimal RNA-Seq quantification

la_dataviz

Slides for LA Dataviz presentation

lintr

Static Code Analysis for R

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

minfi

Devel repository for minfi

MOFA

Multi-Omics Factor Analysis

MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data

MultiAssayExperiment

R package(s) demonstrating management of multiassay data on a set of samples

MultiOmicQC

null

NNLM

Nonnegative Linear Models (NNLM) and Nonnegative Matrix Factorization (NMF or NNMF).

NPBayesHMM

Nonparametric Bayesian Inference for Sequential Data. Includes state-of-the-art MCMC inference for Beta process Hidden Markov Models (BP-HMM). Implemented in Matlab.

obrien_response

Analysis of "Molecular convergence in ex vivo models of Diamond Blackfan anemia"

oldGridExtra

solve a problem I'm having for BioC2015 and elsewhere

ozymandias

Look on my works, ye Mighty, and despair... just kidding, it's a slightly better meth lab

ozymandiasData

AOCS and other data for BioC2015 workshop

PAMES

Tool to estimate purity of tumor samples exploiting DNA Methylation data

Paradigm

PAthway Representation and Analysis by Direct Inference on Graphical Models

pocrmplot

fussing with PO-CRM and plotting the actual dose escalation path (AACR workshop)

powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

RBioFabric

An R implementation of the BioFabric network visualization tool

rcloud

RCloud is an HTML5 frontend for collaboratively developing and sharing R scripts

regulatoR

R package to detect correlated changes across phenotypes by sparse filtered regression

restfulSE

demonstration of SummarizedExperiment with assay component retrieved from remote HDF5 server

rGammaGamma

Gamma convolutions for background correction

rigraph

igraph R package

roxpkg

demonstration of weirdness observed in roxygen2 5.0.0

Rscripts

contents of my ~/.Rscripts folder, minus private ones with account numbers. I'll probably package these.

rSection

port of DSection to R using cppBugs and a DP prior on k

rsite

A clean, modern website for R using Bootstrap3 and Slidify

rStructurama

hooks Structurama into R via Rcpp

RTCGAToolbox

null

rtsne

An R package for t-SNE (t-Distributed Stochastic Neighbor Embedding)

schemas

Work on data models and APIs for Genomic data.

sciclone

An R package for inferring the subclonal architecture of tumors

sesame

R package for analyzing Infinium DNA methylation BeadChip data

seurat

R toolkit for single cell genomics

Shannon

RNA-Seq

sigopt-examples

Optimization Examples with SigOpt

simpleSampleSearch

a trivial R package to search GEO and SRA without the huge hassle of the NCBI interfaces

simulatorZ

simulates collections of independent genomic data sets, and performs training and validation with predicting algorithms

sleuth

Inspect kallisto RNA-Seq output

spark-examples

Example spark integrations.

speedseq

A flexible framework for rapid genome analysis and interpretation

squeakr

Squeakr: An Exact and Approximate k -mer Counting System

ssizeRNA

Sample Size Calculation for RNA-Seq Data

ssizeRNA-1

null

structSSI

Source code for R package structSSI, implementing the Hierarchical FDR procedure and Group Benjamini-Hochberg procedure.

Submodular-Selection-of-Assays

null

svaseq

Analysis for svaseq paper

svtyper

Bayesian genotyper for structural variants

tapkee

A flexible and efficient ?++ template library for dimension reduction

tensorBF

Working mirror of tensorBF for my own purposes

TENxGenomics

Interface to 10x Genomics' 1.3 m single cell data set

tomasetti

A quick and dirty reanalysis of Tomasetti & Vogelstein 2015, in particular Point 3 of their arXiv rebuttal.

ttriche.github.io

visual cv

ucscBeacon

A GA4GH Draft Beacon implementation

upipe

null

uscgdsr

R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS)

user2014.github.io

UseR 2014 Web Pages

vcflib

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

vg

tools for working with genome variation graphs

VisualResume

An R package for creating a visual resume

Commits To