Search Results for "base-files" - Page 10

Utility to convert PED genome file into RAW SNP format. Creates multiple files per person. Supports big files. The same conversion utility has been included into "aisconvert" toolkit, so this project is rather deprecated.

BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.

Luminous is a set of programs and C++ classes to handle Illumina GTC files.

A set of utilities to handle individual-level genotype data files

Writing parameter sets for mutant models coded in BlenX is a tedious procedure that involves the mechanical (and error-prone) process of dealing with textual files. GeMPS offers a GUI that simplifies the generation of combined parameter sets.

A simple tool to import the diff, gtf and tracking files from cufflinks, cuffcompare, cuffdiff into a new sqlite database for data mining.

Adjusting PKL-Files derived from MS-experiments. The development of the project has been MOVED TO https://github.com/binfalse/adjustpkl

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.

Skittle is a 2D visualization of genome sequence files. The program assigns four colors to the four nucleotides and text wraps the sequence to create a 2D picture based on the DNA sequence. Great for researching tandem repeats and chromosome structure. Compiled downloads available at http://dnaskittle.com/ Source maintained at https://github.com/josiahseaman/skittle

IMAS is a Visual Analytics system for the discovery of knowledge in genomic information. IMAS enables genomic scientists to rapidly analyze and visualize a set of microbial genomic sequences using tools such as Glimmer, Blast, Clustal-W, Primer3.

Small set of utilities used by the 2010 iGEM Mexico-UNAM-CINVESTAV Team to automate biobricks from files

These scripts written in Python allow you to convert fasta files into multifasta file and vice versa.

Phylogenetic Representativeness is a method for estimating adequacy of taxon sampling for phylogenetic studies. Through a series of statistics generated by PhyRe, it is possible to evaluate taxon coverage within a given group.

BigBang/Horizon is a proteomics data analysis pipeline with focus on the shotgun LC/MSMS workflow.

Common code developed by researchers in the Edwards Bioinformatics Group at SDSU. This code is free for everyone to use. It is our base code that we provide on an as-is basis. Please let us know if you use the code or have questions/comments

Herbar Ligero es una aplicación diseñada para digitalizar colecciones botánicas de una manera rápida y sencilla. Se concibe con una configuración mínima en única base de datos para trabjar con Entradas rápidas, Nombres científicos y Localidades.

NeuraPy is now hosted on github This is a collection of Python modules that read files encountered in neuroscience experiments. Included are modules to read lablib files and modules to read Cyberkinetics Cerebus system .nev and .ns3 files

A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.

An Emacs module to simplify creating and editing NONMEM files.

Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates coverage...

The goal of EPT is to get track representations from the clipboard (put there by Ethovision) and to automatically save the serie of images while incrementing a value in their filename.

A simple tool for finding the positions and melting temperatures (Tm) of DNA primers using the base-stacking method. Outputs an HTML file of the original sequence where the start position of each primer is a link. Hover-text gives Tm and length.

A fast motif finder base on statistical significant K-mer for DNA sequence.

vcif is an open source software for validation of Crystallographic Information Files. It supports lexical, parser and dictionary validation (DDL 1 and 2 are fully supported, DDLm draft partially supported)

cifget is a DDLm dictionary import expansion utility, which generates expanded dictionaries that could be used when reading, writing, or validating CIF files