Pinned Repositories
Metagenome-profile
For automatic download of metagenomic samples and profiling using Anvi'o
Refseq_pangenomics
pangenomics of all Bacteroides fragilis Refseq genome assemblies
ShaiberAlon's Repositories
ShaiberAlon/Refseq_pangenomics
pangenomics of all Bacteroides fragilis Refseq genome assemblies
ShaiberAlon/2018_microbial_omics_workshop
A workshop for the first year biophysical sciences graduate students at the University of Chicago
ShaiberAlon/alons-online-rep
general use rep for me to dump stuff online
ShaiberAlon/anvi-export-locus-blog
Files for the blog re: anvi-export-locus
ShaiberAlon/cancerGenomics
Cancer Genomics related stuff
ShaiberAlon/casereport
Genome graph based case reports
ShaiberAlon/Conpair
Concordance and contamination estimator for tumor–normal pairs
ShaiberAlon/COVID19
A place to put COVID19 public resources
ShaiberAlon/dotfiles
my dotfiles
ShaiberAlon/dotfiles-1
ShaiberAlon/dpclust3p
Dirichlet Process Clustering Pre-Processing Pipeline
ShaiberAlon/dryclean
Irons out wrinkles in noisy coverage data using robust PCA
ShaiberAlon/fgsea
Fast Gene Set Enrichment Analysis
ShaiberAlon/fishHook
R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.
ShaiberAlon/fragCounter
GC and mappability corrected fragment coverage for paired end whole genome sequencing
ShaiberAlon/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.
ShaiberAlon/gGnome.js
ShaiberAlon/idba
ShaiberAlon/loosends
Loose ends in cancer genome structure
ShaiberAlon/mysetup
Things I do to setup my Mac
ShaiberAlon/Rlife
ShaiberAlon/rna-seq
Playing with some transcriptomic data
ShaiberAlon/SeismicAmplification
Scripts written for the manuscript "Chromothripsis followed by circular recombination drives oncogene amplification in human cancer"
ShaiberAlon/shaiber.github.io
ShaiberAlon/ShaiberAlon
COVID-19
ShaiberAlon/shtools
Helper R functions
ShaiberAlon/SnakeChunks
Modular blocks to build Snakemake workflows for reproducible NGS analyses
ShaiberAlon/snakemake-vim
vim syntax for snakemake - copied from the official snakemake repo
ShaiberAlon/SnakeSki
Collection of Snakemake workflow for data analysis jobs commonly done in mski Lab
ShaiberAlon/stunning-disco
self-made python packages