Search Results for "python data analysis" - Page 2

wEMBOSS is a Web interface for the EMBOSS software package for biological sequence analysis. Under wEMBOSS each user has a private workspace (UNIX home directory) on the server, where he can permanently store his data and organize them in projects. The companion suite wrappers4EMBOSS allows to integrate under EMBOSS a number of popular bioinformatic software suites as BLAST, CLUSTAL and MRS.

The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes.

OpenCV powered image stack analyser for data extraction and preparation. Can be used in conjunction with nanocalcFX. You can get sample data at the NISA homepage. Currently in pre-alpha state.

These are Python scripts plus C/C++ programs for automating the reference free genomic analysis described in: Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11). http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995 Analytical concept conceived by CHCannon and CSKua.

BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files

CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms. An overview of the CisPlusFinder can be found in the flowchart.tif file and is described in the following publication: Pierstorff, N., C.M. Bergman & T. Wiehe. (2006) Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics 22:2858-2864. http://www.ncbi.nlm.nih.gov/pubmed/17032682

This is a c-library that provides tools for advanced analysis of electrophysiological data. It features denoising, unsupervised classification, time-frequency analysis, phase-space analysis, neural networks, time-warping and more.

Flow Investigation using N-Dimensions (FIND) is a program designed for analysis and visualization of Flow Cytometry data. FIND focuses specifically on automated population discovery (clustering) methods. The project targets both users and developers.

Metaboflux is a generic approach for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments, to increase the biological relevance of the model.

Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.

A population-based method for DNA copy number analysis: recurrent copy number aberration indentification in multiple samples (with no need of single-sample calling). Developed for a quick analysis of high resolution and large population data.

Stand-alone software tool for the interactive CE analysis of microarray data. The software is a user-friendly and allows on-the-fly study of CE

The C Protein Folding Library is a minimalistic, high-performance modular library of C functions and data structures for computing folding simulations of proteins on a wide variety of computer hardware.

Neurospaces is a development center for tools in computational neuroscience. See http://www.neurospaces.org/

The BioArray Software Environment (BASE) v1.2 is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. PrognoChip-BASE extends BASE v1.2.16, providing more functionalities.

RasTop is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules based on the popular Rasmol software. The program is aimed at the rapid visualization and analysis of molecules.

Video monitoring tool for insect analysis

BLASTgres is a set of modules that can be added to PostgreSQL for data management of biological sequences. It extends PostgreSQL with datatypes for sequence information and middleware for dynamic access to sequence analysis tools & services like BLAST.

QTL Reaper analyzes data from progeny of a genetic cross in experimental plants or animals. It seeks the location of genes that affect a heritable trait, and it is specially designed for analysis of gene expression measurements.

Tools for comparative sequence analysis. Includes FamilyRelations (GUI) and a C++ toolkit/Python wrapper for doing fixed-width-window analyses.

CompLearn is a general-purpose compression-based machine learning system that uses data compression to learn or data mine patterns in arbitrary data.

Genetic analysis programs for affected sibling pair data and discrete traits, including multipoint exclusion mapping, map distance estimation, transmission disequilibrium testing, and relationship validation