Search Results for "linux command" - Page 3
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Showing 102 open source projects for "linux command"
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A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).
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Genetic data converter
Convert genetic data for hapmixmap software
Genetic data converter, for hapmap.org and hapmixmap data formats. Reads data in tabular format and writes in hapmixmap format. It's possible to add extensions to output different data formats. -
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EASER
Ensembl Easy Sequence Retriever
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. -
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CDSbank
multi-sequence extraction, filtering & formatting
CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5’ and 3’ ends, full taxonomic data, and a heuristic to rank the scientific interest of a species. This rich information allows fully automated data set preparation with a level of sophistication that meets or exceeds manual processing. Defaults ensure ease of use for typical... -
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A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper
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ARDEN
Specificity Control for Read Alignments Using an Artificial Reference
We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation. -
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein... -
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CoNIFER
Homepage for CoNIFER (Copy Number Inference From Exome Reads)
CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. -
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Prediction of MHC class I- and MHC class II-restricted T-cell epitopes. Prediction of proteasomal/immunoproteasomal processing of antigens. Prediction of peptide-TAP binding.
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An... -
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brocc
BLAST Read and OTU Consensus Classifier
NOW HOSTED ON GITHUB: https://github.com/kylebittinger/brocc Old releases are kept here for archival purposes. -
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GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is... -
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QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.
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The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.
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AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data.
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We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.
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Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.
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ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.
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FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra
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Text2Genome is a set of scripts to extract nucleotide sequences from scientific articles and to map them to genomes and genes using a local alignment algorithm (BLAST/BLAT)
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Metmask has moved to github http://github.com/hredestig/metmask Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.
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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.
