Rob Patro's repositories
txome-toolbox
Random code that's helpful when doing transcriptomics things!
randomcode
pretty much what it says
RSEM
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
sparsehash
Automatically exported from code.google.com/p/sparsehash
spdlog
Super fast C++ logging library.
transcriptome_quantification
scripts and data for the comparison found at http://sjcockell.me/2015/05/18/alignment-free-transcriptome-quantification/
FacultyHiringPaper
A repository to test out some thoughts / ideas related to the paper "Systematic inequality and hierarchy in faculty hiring networks"
piquant
A pipeline to assess the quantification of transcripts
GHOST
Global Network Alignment using Multiscale Spectral Signatures
GHOST-CPP
Rewriting (at least some) of GHOST in C++
course
Source code for the applications presented in the course "Geometry Processing with Discrete Exterior Calculus"
quip
Compressing next-generation sequencing data with extreme prejudice.
readfq
Fast multi-line FASTA/Q reader in several programming languages
rws
Python implementation of Random Walk with Resistance (RWS) for PPI filtering
redwood
A C++11 library for dealing with phylogenetic trees (and later, maybe, phylogenetic networks).
seqan-mirror
Git mirror for the SeqAn project.
Pythy
Having it all now: Pythy syntax for C++11
Jellyfish
Fork of the jellyfish kmer counter. Here is the description copied from their site: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish stats" command. See the documentation below for more details.
ScalaIntro
A small set of Scala examples & links for a brief Scala introduction given at UMD