Search Results for "x86_64-linux-gnu" - Page 3
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Showing 937 open source projects for "x86_64-linux-gnu"
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miRDP2
Accurately and fast analyzing microRNAs transcriptome in plants
miRDeep-P2 (miRDP2) is developed to accurately and fast analyze microRNAs (miRNAs) transcriptome in plants. It is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm. We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed NGS data with superior speed. By incorporating newly updated plant miRNA... -
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ASGARD
Metabolic reconstruction from DNA or protein sequences.
ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS. -
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This is software to create web dictionaries, esp. for Esperanto like Reta Vortaro (http://reta-vortaro.de). A dictionary is made from articles written in a special XML dialect by transformations using XSLT, ant and some Java code.
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Allelome.PRO
A pipeline to define allele-specific genomic features
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... -
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MitoSAlt
Identification of mitochondrial structural alterations
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. -
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PINCIS
PINCIS.pl is a Perl bioinf. script to analyze PICS data
PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be... -
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New Debian package available 30th April 2021, lots of bugs corrected. Simple system for displaying civic features, opportunities and problems on a rasterised map. Currently to map 'informal gardening' and foraging for useful items on the street. Simple to set up and use. Can be parametrised for specific usage. Installation description, to be expanded in: https://sourceforge.net/p/datamap/wiki/Installation/
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wxProdOp
NMR Product Operator Calculator
The program does nmr product operator calculations for one, two, three and four spins. Receiver phase cycling is possible in conjunction with pulse phase cycling to simulate coherence pathway selection. An extensive manual and help files are included. Currently running under Linux and Windows. -
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed. Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated... -
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TA-Lib.git: Technical Analysis Library
Mirror of the TA-Lib project using a Git repository
This project is intended to provide Git access to the code of the original project, TA-Lib, which uses Subversion. It is intended for system integrators wishing to use TA-Lib in their Git-managed project through Git submodules or subtrees. No actual development is being done here; all development happens in the original project. -
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mapska
The Murder Accountability Project's Serial Killer Algorithm
A much improved Linux/Perl implementation of the Murder Accountability Project's Serial Killer Algorithm. This module was tested with the "SHR76_19.csv" available from www.murderdata.org/p/data-docs.html. This module provides functions to prepare the data, upload to a database and view the identified clusters. Download SHR76_19.csv (23/03/2021) - https://www.dropbox.com/s/ye37woe6et05qgs/SHR76_19.csv.zip?dl=1 For information on this algorithm and the Murder Accountability Project please... -
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ModST
A tool to search post-translational modifications in a blind mode
ModST (pronounced as modest) is a tool to search post-translational modifications (PTMs) in mass spectrometry data in an unrestrictive manner. It can search for hundreds of modification without any user provided information for variable modifications. Due to data level parallelization implemented through perl it is fast, portable and easy to use to identify and analyse PTMs in MS/MS data. -
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chklinks is a non-threaded Perl link checker. It helps finding broken links on your website. It does not raises many simultaneously connections for its job, run out of the resources and crash your system in a moment.
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Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.
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ApVSys is a general open-source wrapper designed for engineering Unix/Linux environment..It provides a way to use and manage simultaneously different versions of applications (engineering tools, compilers, debuggers simulators, ... ).
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Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.
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MANTI.pl / muda.pl
muda.pl - MQ unified data assembler
-------- ATTENTION START: RENAMING muda.pl was renamed to MANTI.pl with v3.7, project development can be tracked on the MANTI project page on sourceforge.net. Old versions remain here for archival purposes. -------- ATTENTION END muda.pl is an evaluation script (written in Perl) without great dependencies. It congregates information from 4 different MaxQuant output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data... -
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C-squares
Concise spatial query and representation system (c-squares)
C-squares is an easily implemented method for storage, querying and display of spatial data locations, based on a hierarchical, grid-based representation of the Earth' surface. Source code for encoding, decoding, mapping, etc. is provided via this site. Additional support is available by contacting the system developer, Tony.Rees@marinespecies.org; see also the c-squares home page at http://www.cmar.csiro.au/csquares/ . -
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software... -
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MMAP
Multi-core Method for Analysis Pipelines
For more information, please see home page. -
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through... -
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FastaTools
Performs several operations to Fasta protein databases
FastaTools performs several operations to Fasta protein databases. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/fastatools/code/ci/default/tree/README.md Or you can download the Documentation an Tutorial PDF file in the Files section: https://sourceforge.net/projects/fastatools.lp-csic-uab.p/files/FastaTools%20Documentation%20and%20Tutorials.pdf - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M.,... -
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OmssaGUI
GUI front-end for OMSSA
GUI front-end for the OMSSA proteomics search engine. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/omssagui/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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SequestGUI
GUI front-end to sequest.exe
GUI front-end to sequest.exe proteomics search engine, developed in Perl. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/sequestgui/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124