Alon Shaiber's repositories
Refseq_pangenomics
pangenomics of all Bacteroides fragilis Refseq genome assemblies
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
Conpair
Concordance and contamination estimator for tumor–normal pairs
COVID19
A place to put COVID19 public resources
dotfiles
my dotfiles
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.
loosends
Loose ends in cancer genome structure
mysetup
Things I do to setup my Mac
rna-seq
Playing with some transcriptomic data
SeismicAmplification
Scripts written for the manuscript "Chromothripsis followed by circular recombination drives oncogene amplification in human cancer"
ShaiberAlon
COVID-19
shtools
Helper R functions
SnakeChunks
Modular blocks to build Snakemake workflows for reproducible NGS analyses
snakemake-vim
vim syntax for snakemake - copied from the official snakemake repo
SnakeSki
Collection of Snakemake workflow for data analysis jobs commonly done in mski Lab
stunning-disco
self-made python packages