Best Bioinformatics for Linux
Genepidgin is a suite of Python tools that assist in evaluation and assignment gene product names. There are three primary components:genepidgin *cleaner* standardizes gene names per UNIPROT naming guidelinesgenepidgin *compare* compares...
STEPS is a package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie's SSA, extended to deal with diffusion of molecules over the elements of...
TRMiner is a Python utility that aims at scientific data curators. It allows to rapidly prune large collections of scientific publications to sentences relevant for a given mining goal.This is achieved in two steps. First, texts are tranlated into...
The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems.What we are trying to do is to create a framework for testing, and a core...
Staden Package is a fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.On the Gap4 front there have been several minor joining relatedimprovements in how it scores joins in Find...
AREM is a based on MACS (Model Based Analysis for ChIP-Seq data).High-throughput sequencing coupled to chromatin immuno- precipitation (ChIP-Seq) is widely used in characterizing genome-wide binding patterns of transcription factors, cofactors, chromatin...
seriesoftubes is an extended pipeline for Solexa ChIP-seq data.Package...
MetagenomeDB is a Python library designed to easily store, retrieve and annotate metagenomic sequences. MetagenomeDB act as an abstraction layer on top of a MongoDB database. It provides an API to create and modify and connect two types of objects,...
Seal is a Python module that provides sequence alignment on Hadoop.Seal is a of MapReduce application for biological sequence alignment. It runs on Hadoop (http://hadoop.apache.org) through Pydoop (http://pydoop.sourceforge.net), a Python MapReduce and...
MISO (Mixture of Isoforms) is a probabilistic framework written in Python that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.By modeling the...
