Open Source Cygwin Bio-Informatics Software - Page 2
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Bio-Informatics Software for Cygwin
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SWATnalysis
Analysis of SWAT output files
Runs the Soil and Water assessment Tool (SWAT), and analyzes associated output files. Converts archaically formatted SWAT output files into more user friendly excel csv files, performs graphical analysis, calculates area weighted precipitation values, and performs statistical analysis of observed data versus simulated data. -
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ScreenSifter
ScreenSifter is a unique tool for RNAi Screen analysis and management
ScreenSifter can help you in managing all your RNAi screens related projects in organized fashion. ScreenSifter, to perform the sequential, user friendly, guided, and advanced statistical analyses of RNAi screening results. User can upload their raw signal intensities and will avail complete quality control of screen, hit selection, plotting of hit genes with gene ontology, comparing of replicates or comparing of channels. In addition, ScreenSifter has visualization tools to plot specific genes 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 -
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Seqshell
A JAVA GUI for performing the function of Tophat and Cuffdiff
Combines the Tophat and Cuffdiff functions in one GUI interface. tophat and cuffdiff are required to be pre-installed in the system. By modifying the program, it can be used to execute any command line programs even R packages since R can also be run from commandlines. New functions: Batch processing function for Tophat. You can now execute as many mapping jobs as you want with tophat. This program will save the output into separate folders. An alert email will be sent to your email address when the job is done. (You will need to modify the source code to change the content to meet your special needs) Run-time information will be displayed in a JAVA output window. -
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TRF_Pathway
A Random Forest based Pathway association analysis tool
The TRF-pathway package implements the powerful two-stage random forest based pathway analysis. The manuscript discussing the method is currently under revision at PLoS One. -
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Tools for T-RFLP data analysis
VB macros and a template for the analysis of T-RFLP data using Excel.
A collection of Visual Basic macros and a template for the analysis of terminal restriction fragment length polymorphism data using Microsoft Excel. -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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XNBC: neurobiology simulation tool
XNBC is a graphic application to simulate biologic neural networks.
XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows. Web site : http://ticemed-sa.upmc.fr/xnbc/ All recent versions are on this site. -
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biojazz
In silico evolution of biochemical networks.
In silico evolution of biochemical networks using a genetic algorithm combined with a rule-based biochemical network model. -
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BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.
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Updated 2022-06-11 added option to allow use of atoms other than C-alpha Updated 2021-11-29 to enable compilation on stricter compilers. Ab Initio protein structure prediction methods generate numerous structural candidates, which are referred to as decoys. Calibur is an efficient tool for finding the decoy with the most number of neighbors within a threshold distance. If you prefer to use GitHub, go to https://github.com/kalngyk/calibur
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Here is a repository of libraries automatically generated by Patlac::Xml2cpp software. All of these libraries are c++ translation of their respective xsd schema. They include classes with accessors, saxparser with iteration mode and xml serialization.
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erne
ERNE - Extended Randomized Numerical alignEr
We present ERNE (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners), -
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fast_count_multi
Extremely fast NGS read counter
Counts NGS read alignments against GTF annotations in a multithreaded and scalable fashion. Benchmark: 8 core 1M annotations for 2Gb sorted reads ~30 seconds compared to ~28 minutes for bedtools multicov. Files include: fast_count_multi - reports all counts and RPKM, multithreading support fast_count_deseq - reports gene counts in deseq compatible format, multithreading support fast_count - reports all counts with no multithreading support. usage ./fast_count_multi num_threads gtf_file bam_file(s) > output Requires bamtools API library at run time, and c++0x for compile. git clone https://github.com/pezmaster31/bamtools cd bamtools mkdir build cd build cmake .. make export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path to/lib g++ -I bamtools/include/ -L bamtools/lib/ -o fast_count_multi fast_count_multi.cpp -lz -lbamtools -fpermissive -pthread -std=c++0x -
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gene2path
A tool to study fish gene pathways by search of orthologous genes
Most of the gene regulation pathways data from experiments are drawn from humans or from species commonly used as experimental animal models. Accordingly, the software packages to analyse these data on the basis of specific gene identification codes (IDs) or accession numbers (AN) are not easy to apply to other organisms that are less characterized at the genomic level. Here, we have developed the Gene2Path programme which automatically searches pathway databases to analyse microarray data in an independent, species-specific way. We have illustrated the method with data obtained from an immune targeted rainbow trout microarray to search for orthologous pathways defined for other well known biological species, such as zebrafish, although the software can be applied to any other case or species of interest. The Gene2Path software allows the automated searching of NCBI databases and the straightforward visualization of the data retrieved based on a graphic network environment. -
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SaskSAGE is package designed to exploit SAGE data. Csage is employed to identify and match SAGE tags in a biologically meaningful manner. Tags are analyzed for significance using a Chi squared test for independence between TAG and treatment.