Search Results for "shell command"

https://sourceforge.net/p/contools/contools/ci/master/tree/README.md https://sourceforge.net/p/contools/contools/ci/master/tree/README_EN.txt https://sourceforge.net/p/contools/contools/ci/master/tree/README_EN.deps.txt https://sourceforge.net/p/contools/contools/ci/master/tree/changelog.txt

miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04

RefDB is a reference database and bibliography tool for SGML, XML, and LaTeX documents, sort of a Reference Manager or BibTeX for markup languages. It is portable and known to run on Linux, Free/NetBSD, OSX, Solaris, and Windows/Cygwin.

Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analysed imprinted...

MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided.

Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.

BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files for...

Please note that OWFS source code, and all Issue/Tickets/merge requests have now been moved to https://github.com/owfs/owfs/. Developer mailing lists will still be kept at Sourceforge. ---- OWFS -- 1-Wire file system. Use the Dallas 1-Wire and iButton chips with standard filesystem commands. Create temperature loggers. Monitor everything. OWHTTPD -- same system, only used as a light weight web server. OWFS is also ported to embedded routers, Mac OSX and Windows. Basically you can use these...

HitKeeper is a database application for use in BioInformatics. It deals with "hits" (predicted features) on biological sequences (protein, DNA), handles incremental updates effectively, supports taxonomy, and provides original query tools.

Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.

MARF is a general cross-platform framework with a collection of algorithms for audio (voice, speech, and sound) and natural language text analysis and recognition along with sample applications (identification, NLP, etc.) of its use, implemented in Java.

IRSTLM is no more supported on SourceForge. Please visit the new IRSTLM official website: http://hlt-mt.fbk.eu/technologies/irstlm IRSTLM: A tool for the estimation, representation, and computation of statistical language models. IRSTLM, the IRST Language Modeling Toolkit, features algorithms and data structures suitable to estimate, store, and access very large n-gram language models. Our software has been integrated into a popular open source Statistical Machine Translation decoder...

Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.

Statistics modules in Perl Data Language, with a quick-start guide for non-PDL people. They make the PDL shell work like R, but with PDL threading (fast automatic iteration) of procedures including t-test, linear regression, and k-means clustering.

Various tools for creating annotated parallel corpora including pre-trained tagging and parsing models for various languages, sentence alignment tools and word alignment tools. Uplug also includes a web-based interface for interactive sentence and word alignment and scripts for indexing and querying parallel corpora using the Corpus Work Bench CWB. Download 'uplug-main' first and then add other packages.

ForeRunner X01 toolkit provides an easy access to Forerunner 201/301/305/305E GPS-units. There are multiple command line tools to read data from GPS into database and tools to export data in different formats like gpx and tcx.

This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers.

Development and support of OCFA have been discontinued. the code has moved to these github repositories: https://github.com/DNPA/OcfaLib https://github.com/DNPA/OcfaArch https://github.com/DNPA/OcfaJavaLib https://github.com/DNPA/OcfaModules https://github.com/DNPA/OcfaDoc If you are interested in contributing to ongoing work on the creation of a community maintained OCFA inspired computer forensic framework, please join the Mattock/MattockFS community page on...

CPU Balance is a Perl script to balance the CPU usage among users. It will allocate CPU resource to each user equally only by the command renice, no matter how many processes/threads a user runs. ################ # Basic Renice Goal ################ 1. User-based balance: every user get the same cpu percentage if they ask for more; 2. all the jobs of one user has the same NI; 3. NI of all jobs tend to move as large as possible when balanced; 4. No sudden change on NI. max change of NI...

FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.

A set of Unix command line tools for quick and convenient batch processing of tabular text files (a.k.a., tab-delimited, csv, or flat file format) with a header line. Provides delimiter and compression detection, column reference by name. * tblmap: per-line ("map") computation: derive columns through an expression, delete, reorder, filter rows. * tblred: compute ("reduce") aggregations (e.g., sum, average) over groups defined by key columns. * tbldesc: Summarize columns in file (e.g...

A logging shell that can log commands from a shell. Designed to act as an automated lab-book for people that conduct experiments in their standard shell environments. Users can log and re-run experiments with little/no manual effort or interference.

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

SURFnet IDS, a Distributed Intrusion Detection System (D-IDS). The goal is to provide an early warning system which lets system administrators correlate known and unknown exploits to attacks directed towards their networks.

ModelicaFloChrt is a script/Perl process that extracts information from Modelica library html help files and generates flow charts of module connectivity in eps and pdf formats.