Search Results for "bioinformatics with python cookbook" - Page 2

Mitomaker is a pipeline wrapper, result analyzer and automated annotator, written in Python v2.7, that, with the help of other programs, builds, analyzes, looks for the best build and annotates target genomes (such as mitochondria and cloroplast). It could be used with other targets, such as specific genes, or transcriptomes, even though that is not it's primary goal, nor thoroughly tested. After various attempts to build different mitochondrial genomes in the lab I studied, a general...

A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).

The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE.

BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby...

Maldonado E, Khan I, Philip S, Vasconcelos V, Antunes A (2013) EASER: Ensembl Easy Sequence Retriever. Evolutionary Bioinformatics, 9:487-490. doi: https://doi.org/10.4137/EBO.S11335.

... or gene groups in the screen data. ScreenSifter also provides Gene Set Enrichment Analysis (GSEA), protein-protein interaction directly on the plot. Publication: ScreenSifter: analysis and visualization of RNAi screening data Pankaj Kumar, Germaine Goh, Sarawut Wongphayak, Dimitri Moreau and Frédéric Bard BMC Bioinformatics. 2013 Oct 3;14(1):290. http://www.biomedcentral.com/1471-2105/14/290/abstract

AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data.

A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.

NumericalFISH is a bioinformatics graphical tool for easy analysis of BLAST or BLAT results, especially aimed at the study of duplications or segmental duplications.

Object oriented software classes and programs implemented in multiple software languages for biological informatics and bioinformatics applications.

PLEAC (Programming Language Examples Alike Cookbook), is an effort to implement the Perl Cookbook solutions in other programming languages.

A random recipe generation engine, built as a Python CGI.

A set of bioinformatics tools for the open source bio-informatics platform "birch"

CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.

Cyrille is an workflow management system aimed at high throughput pipelines in Bioinformatics.

A lightweight, browsing-based, 100% Python, federated data integration framework. Users may create custom schemas for disparate sources, query and expand results across sources to find related data; for use in fields such as bioinformatics and datamining

A Python library bringing together utilities I've written over the years for work in bioinformatics and biostatistics, which should be generally applicable outside these fields as well. Focuses on string processing, DBI, and math.

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr.

The dispatcher provides loosely-coupled message passing between Python objects (signal senders and receivers). It began as one of the highest-rated recipes on the Python Cookbook website

PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.

E-Cookbook is an electronic cookbook or recipe organizer. It will replace the old tattered cookbook in your kitchen. Easily decide on something to make for dinner, or see what you can make based on the ingredients in your refrigerator.

A project to develop an integrated and open bioinformatics framework and environment.

SeqFreed is a bioinformatics desktop. It provides efficient access to sequence data and gene features, a customizable command line interface to locally installed bioinformatic tools and flexible display of either text or images in different page modes.

openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database