Project code for Fungal genomics, comparative, and related research at the Stajich lab at UC Riverside.

<wiki:toc> <br> ==BEDTools Summary== The BEDTools utilities allow one to address common genomics tasks such as those below, as well as develop sophisticated pipelines that answer complicated research questions. # Intersecting two BED files in search of overlapping features. # Merging ove...

TCGA2S3DB is an infrastructure that exposes data from The Cancer Genome Atlas (TCGA) using Semantic Web Formalisms, specifically, as a SPARQL endpoint. Experimental data, such as the one being generated by the TCGA project, is often intrinsically complex and very heterogeneous. For that reason, it ...

A simple library to store and query genomic features and sequence. * Find neighbors of a given feature up or downstream, or on a given strand. * Use a feature to slice out sequence from an associated fasta file. Genedex uses numpy memmaped arrays for fasta slicing of fasta files without creat...

Segway is a segmentation program for functional genomics data.

bioinformatics stuffs. any feedback or contributions would be *greatly* appreciated i can move code to github/bitbucket to facilitate that if it helps: *NOTE*: as of 2009/10/13 some modules which previously lived here have been moved to [http://bitbucket.org/brentp/biostuff/ bitbucket] * bio...

Yet another population genetics toolkit, this time in python. pgtools is like Rozas' `DNASP`, Thornton's `libsequence`, Cai's `PGEToolbox`, Marchini's `popgen`, but in python. What it does: * parses a few of the usual formats, particularly the output of Hudson's `ms` * computes most of t...

This project includes software and tools to support publication of linked genomic data on the fruit fly (Drosophila). Sub-projects: * [Flybase] * [Bdgp] * [Flyatlas] * [Flyted]

We developed a novel mining pipeline, inGAP, which is guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms.

WormBase is the public database for information on C. elegans and related nematodes.