Search Results for "https" - Page 2
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Showing 51 open source projects for "https"
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
VFS was fullly tested under Ubuntu/Debian system. ** Announcement 1**: VFS is superior to Virus-Clip. https://sourceforge.net/projects/viralfusionseq/files/VFS.vs.Virus-Clip.pdf/download As of 2016, VFS is the only viral integration tool available at NIH HPC system. https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. ... -
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NexStarCtl
Cross platform Perl API to control NexStar compatible telescopes
...This program is a complete console tool to control NexStar telesctopes based on NexStarCtl module. To control network based telescopes nexbridge must be used on the remote site. https://sourceforge.net/projects/nexbridge/ -
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**** This page is not used for this project any longer. *** Please update your bookmarks and go to https://github.com/UUPharmacometrics/PsN
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BamBam
Tools for genomic analysis
...Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball. -
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gladTeX
GladTeX -- embed LaTeX-quality images in HTML
...Additionally, alt-tags are auto-generated which display the LaTeX-equations when the HTML is viewed e.g. with a text mode browser or by someone with vision loss. The project home has moved, please visit https://humenda.github.io/GladTeX -
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OneLDAP is a limited LDAP server that is a proxy to other common protocols, such as POP3 and IMAP. It provides basic SEARCH and BIND functions for standard LDAP authentication. It is based on the shell backend function of OpenLDAP. Release files are available at the project website.
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A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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bsclient
An interactive FTP-like command-line BaseSpace download client
...It has a simple interface simliar to FTP and can be used to easily download files onto a remote server or in any situation when the web-based interface is not accessible or desirable. Please note that current development on this project has moved to GitHub: https://github.com/jvolkening/bsclient -
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ReseqTrack is now hosted at github: https://github.com/EMBL-EBI-GCA/reseqtrack ReseqTrack is a mysql database and perl api for tracking files associated with resequencing projects and running analysis pipelines on resequencing data.
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BatchFusionPrimer
now hosted here: https://github.com/dohalloran
now hosted here: https://github.com/dohalloran -
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Shoal
A lot of fish in a shoal, in a gigantic scientific ocean.
...Shoal Shell Project needs grownup I'm just a student in the university, and the shoal shell just in its begining, if you have any idea about shoal, please contact me from xie.guigang@gmail.com. The Shoal shell needs your professional advice. Try get some help (if you want build the shoal library by yourself): https://sourceforge.net/p/shoal/wiki/Shoal%20Developer%20Guide/ -
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TransGeneScan
TransGeneScan is a gene finding tool for metatranscriptomic sequences
NOTE: TransGeneScan is migrated to Github (https://github.com/COL-IU/TransGeneScan). TransGeneScan is no longer maintained in SourceForge. Please find the latest version in Github. TransGeneScan is a gene finding tool for Metatranscriptomic sequences. TransGeneScan incorporates strand-speci c hidden states, representing coding sequences in sense and anti-sense strands on transcripts in a Hidden Markov Model similar to the one used in FragGeneScan (http://fraggenescan.sourceforge.net/), and can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript. -
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CG-Pipeline
A computational genomics pipeline for prokaryotic sequencing projects
This project has moved to Github! However, please see the Sourceforge wiki for any help. https://github.com/lskatz/cg-pipeline http://cg-pipeline.sourceforge.net/wiki/index.php/Main_Page -
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Protdraw
Create portable, flexible domain drawings of protein sequences
For ProtDraw to work on MacOS Yosemite, you must install a patched Pert Tk. Go to https://github.com/eserte/perl-tk and click the Download zip button. Run the unzip command, cd to the extracted directory and follow the directions in the 'INSTALL' file (using 'sudo' if necessary). ProtDraw creates flexible, easily-interpretable and portable illustrations of the domain structures of input sequences. ProtDraw is accompanied by makeProtDraw, a helper program which runs hmmer3 on a specified set of hidden Markov models and formats results for ProtDraw. ... -
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EXCAVATOR-tool
Tool for detecting CNVs from whole-exome sequencing data
...We recently published on BMC Genomics a novel software package, named XCAVATOR, for the identification of CNVs/CNAs from short and long reads whole-genome sequencing experiments (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/. EXCAVATOR is a novel software package for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR has been published on Genome Biology (http://genomebiology.com/2013/14/10/R120/abstract). #################### ATTENTION!!!!! ... -
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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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ParaSim
Parallelized calculation of molecular similarities
...It does not compute fingerprints by itself but relies on third party software to do so. Basically, all types of structural fingerprints which can be stored in an array of bits (a bitset) can be used by ParaSim. See the Wiki (https://sourceforge.net/p/parasim/wiki/Documentation/) for detailed documentation. FEEDBACK HIGHLY APPRECIATED! -
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SeqWare has moved to GitHub, see https://github.com/SeqWare SeqWare is a project to create a tool set to work with next generation genome sequencers (SOLiD & Illumina). It includes a LIMS, Pipeline, and Query Engine. Check out the wiki link below to see documentation. You can get the source from the Develop link.
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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 G+: https://plus.google.com/communities/102487198908055860744
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This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the following paper: Ehsan Emadzadeh, Azadeh Nikfarjam, and Graciela Gonzalez. 2011. Double Layered Learning for Biological Event Extraction from Text. ...
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An experimental CEP (Complex Event Processing) engine. It implements the event stream processing as a library embeddable in C++ and Perl. Since then it has been renamed to Triceps, so please look at the new location https://sourceforge.net/projects/t
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Phylogentic pipeline written in perl. Use svn to get the latest version. svn co https://bio-hal.svn.sourceforge.net/svnroot/bio-hal/trunk hal
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We moved to https://github.com/sueswe/pzgtools Perl-Programs to extract information (and visualize them with gnuplot) from data-files from the PZG Particle Sampler from "rr-elektronik" (see http://www.rr-elektronik.de). Linux/KDE-version, GUI written in QT or Gambas. Win32-ver: pzg-tools.npage.de
