2018_microbial_omics_workshop

A workshop for the first year biophysical sciences graduate students at the University of Chicago

alons-online-rep

general use rep for me to dump stuff online

anvi-export-locus-blog

Files for the blog re: anvi-export-locus

cancergenomics

Cancer Genomics related stuff

casereport

Genome graph based case reports

configuration_files

conpair

Concordance and contamination estimator for tumor–normal pairs

covid19

A place to put COVID19 public resources

dotfiles

my dotfiles

dotfiles-1

dpclust3p

Dirichlet Process Clustering Pre-Processing Pipeline

dryclean

Irons out wrinkles in noisy coverage data using robust PCA

fgsea

Fast Gene Set Enrichment Analysis

fishhook

R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

fragcounter

GC and mappability corrected fragment coverage for paired end whole genome sequencing

gchain

R class for representing composable syntenic mappings between coordinates of 'omes and allowing nimble lift-over of genomic features and signals through these mappings within a GenomicRanges based framework.

genelearn

ggnome.js

idba

illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).

loosends

Loose ends in cancer genome structure

macg

MACg

medusa

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

metagenome-profile

For automatic download of metagenomic samples and profiling using Anvi'o

mysetup

Things I do to setup my Mac

refseq_pangenomics

pangenomics of all Bacteroides fragilis Refseq genome assemblies

rlife

rna-seq

Playing with some transcriptomic data

seismicamplification

Scripts written for the manuscript "Chromothripsis followed by circular recombination drives oncogene amplification in human cancer"

shaiber.github.io