<![CDATA[BOL: All site bookmarks]]> https://bioinformaticsonline.com/bookmarks/all?offset=1150 https://bioinformaticsonline.com/bookmarks/view/27696/methylkit Fri, 03 Jun 2016 10:09:29 -0500 https://bioinformaticsonline.com/bookmarks/view/27696/methylkit <![CDATA[methylKit]]> methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

Address of the bookmark: https://github.com/al2na/methylKit

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27691/histonedb-20-%E2%80%93-with-variants Fri, 03 Jun 2016 05:06:20 -0500 https://bioinformaticsonline.com/bookmarks/view/27691/histonedb-20-%E2%80%93-with-variants <![CDATA[HistoneDB 2.0 – with variants]]> This histone database can be used to explore the diversity of histone proteins and their sequence variants in many organisms. The resource was established to better understand how sequence variation may affect functional and structural features of nucleosomes. To get started, select a histone type to explore its variants.

More at http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/27685/biodbnet Thu, 02 Jun 2016 11:11:47 -0500 https://bioinformaticsonline.com/bookmarks/view/27685/biodbnet <![CDATA[BioDBnet]]> Database to Database Conversions

db2db allows for conversions of identifiers from one database to other database identifiers or annotations. To use db2db select the input type of your data, changing the input type automatically changes the output options to the ones specific for the input selected. Then select one or more output types and add your identifiers in the ID list box. Set the remove duplicate values to 'No' if you do not want duplicates to be removed. Clicking on submit then returns a table of your inputs matched against all the outputs selected in the exact order as entered. Results can be limited to a particular taxon by entering it's Taxon ID. The performance will vary widely depending on the number of outputs and the options selected. Conversions to a single output with the default options should complete in a few seconds

Address of the bookmark: https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27679/cluego Thu, 02 Jun 2016 09:51:44 -0500 https://bioinformaticsonline.com/bookmarks/view/27679/cluego <![CDATA[ClueGO]]> ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize.

Address of the bookmark: http://www.ici.upmc.fr/cluego/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27479/biogps Mon, 23 May 2016 03:15:46 -0500 https://bioinformaticsonline.com/bookmarks/view/27479/biogps <![CDATA[BioGPS]]> A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.

http://biogps.org/#goto=welcome

Address of the bookmark: http://biogps.org/#goto=welcome

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/27477/cytoscape Mon, 23 May 2016 02:32:00 -0500 https://bioinformaticsonline.com/bookmarks/view/27477/cytoscape <![CDATA[Cytoscape]]> Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

Address of the bookmark: http://www.cytoscape.org/

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/27475/polyphen-2-prediction-of-functional-effects-of-human-nssnps Mon, 23 May 2016 02:27:25 -0500 https://bioinformaticsonline.com/bookmarks/view/27475/polyphen-2-prediction-of-functional-effects-of-human-nssnps <![CDATA[PolyPhen-2: Prediction of functional effects of human nsSNPs]]> PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.

Address of the bookmark: http://genetics.bwh.harvard.edu/pph2/

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/27465/stand-alone-programs-for-bioinformatician Sat, 21 May 2016 22:50:15 -0500 https://bioinformaticsonline.com/bookmarks/view/27465/stand-alone-programs-for-bioinformatician <![CDATA[Stand-alone programs for Bioinformatician]]> This directory contains applications for stand-alone use, built specifically for a Linux 64-bit machine.

For help on the bigBed and bigWig applications see:
http://genome.ucsc.edu/goldenPath/help/bigBed.html
http://genome.ucsc.edu/goldenPath/help/bigWig.html

View the file 'FOOTER' to see the usage statement for each of the applications.

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

]]> Radha Agarkar https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines Sat, 21 May 2016 22:42:16 -0500 https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines <![CDATA[Bpipe - a tool for running and managing bioinformatics pipelines]]> Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

]]> Radha Agarkar https://bioinformaticsonline.com/bookmarks/view/27461/maftools Sat, 21 May 2016 22:40:21 -0500 https://bioinformaticsonline.com/bookmarks/view/27461/maftools <![CDATA[mafTools]]> Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

Address of the bookmark: https://github.com/dentearl/mafTools

]]> Radha Agarkar