ttriche Goto Github PK

abyss

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

adockerfile

for anthony

amlcelloforigin

Data and vignettes with helper functions to determine AML cell-of-origin based on reference cell types.

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-data-insights-projects

awesome-single-cell

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

bamslicer

Slice and dice controlled-access BAMs for thousands of samples

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)

bifurcator

bifurcatoR package

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

bioconductor.org

Source code for the Bioconductor website

biocparallel

Bioconductor facilities for parallel evaluation (experimental)

bioinformatics

Tools for bioinformatics

biscuiteer

a small package of bsseq tools for Biscuit output

bitstarter

buildabiocworkshop

need to practice with this newfangled pipeline

butchr

interested in using diagnostics from this package

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

cell_variation

Code for "Untangling biological factors influencing trajectory inference from single cell data"