<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39372?offset=110 https://bioinformaticsonline.com/bookmarks/view/43685/chipbase-open-database-for-studying-the-transcription-factor-binding-sites-and-motifs Wed, 29 Dec 2021 05:36:03 -0600 https://bioinformaticsonline.com/bookmarks/view/43685/chipbase-open-database-for-studying-the-transcription-factor-binding-sites-and-motifs <![CDATA[ChIPBase: open database for studying the transcription factor binding sites and motifs]]> ChIPBase v2.0 is an open database for studying the transcription factor binding sites and motifs, and decoding the transcriptional regulatory networks of lncRNAs, miRNAs, other ncRNAs and protein-coding genes from ChIP-seq data. Our database currently contains ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species.

Address of the bookmark: https://rna.sysu.edu.cn/chipbase/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/27110/easyfig Fri, 29 Apr 2016 05:49:39 -0500 https://bioinformaticsonline.com/bookmarks/view/27110/easyfig <![CDATA[Easyfig]]> Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig.  Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

Address of the bookmark: http://easyfig.sourceforge.net/

]]> Poonam Mahapatra https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 Thu, 12 May 2016 13:49:41 -0500 https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 <![CDATA[Release Notes for Genome Workbench 2.10.5]]> New Features in latest release

  • New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
  • New export function for BAM/cSRA coverage graphs (Tutorial)
  • New export function for alignments GFF3 format ((Tutorial))
  • Tree View: implemented new export mode based on selections (tutorial coming)
  • Tree View: added support for distance based circular trees
  • Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
  • Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)
]]> Jit 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/27841/covcal-coverage-read-count-calculator Wed, 15 Jun 2016 18:08:13 -0500 https://bioinformaticsonline.com/bookmarks/view/27841/covcal-coverage-read-count-calculator <![CDATA[CovCal: Coverage / Read Count Calculator]]> Coverage / Read Count Calculator

Calculate how much sequencing you need to hit a target depth of coverage (or vice versa).

Instructions: set the read length/configuration and genome size, then select what you want to calculate.

Written by Stephen Turner, based on the Lander-Waterman formula, inspired by a similar calculator written by James Hadfield. Coverage is calculated as C=LN/G and reads as N=CG/L where C = Coverage (X),L = Read length (bp), G = Haploid genome size (bp), and N = Number of reads. Source code on GitHub.

Address of the bookmark: http://apps.bioconnector.virginia.edu/covcalc/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30971/hiveplot Thu, 16 Feb 2017 11:39:34 -0600 https://bioinformaticsonline.com/bookmarks/view/30971/hiveplot <![CDATA[HivePlot]]> The hive plot is a rational visualization method for drawing networks. Nodes are mapped to and positioned on radially distributed linear axes — this mapping is based on network structural properties. Edges are drawn as curved links. Simple and interpretable.

The purpose of the hive plot is to establish a new baseline for visualization of large networks — a method that is both general and tunable and useful as a starting point in visually exploring network structure.

More at http://www.hiveplot.com/

Address of the bookmark: http://www.hiveplot.com/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34678/svfinder-tool-for-detecting-genomic-rearrangement-form-dna-seq-data Thu, 14 Dec 2017 15:51:40 -0600 https://bioinformaticsonline.com/bookmarks/view/34678/svfinder-tool-for-detecting-genomic-rearrangement-form-dna-seq-data <![CDATA[SVfinder: Tool for detecting genomic rearrangement form DNA-seq data]]> SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Address of the bookmark: https://github.com/cauyrd/SVfinder

]]> Robert M Willioms https://bioinformaticsonline.com/bookmarks/view/36012/gmol-an-interactive-tool-for-3d-genome-structure-visualization Wed, 21 Mar 2018 12:25:20 -0500 https://bioinformaticsonline.com/bookmarks/view/36012/gmol-an-interactive-tool-for-3d-genome-structure-visualization <![CDATA[GMOL: An Interactive Tool for 3D Genome Structure Visualization]]> GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.

Address of the bookmark: https://www.nature.com/articles/srep20802

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx Sun, 31 May 2020 02:01:14 -0500 https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx <![CDATA[SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.]]> SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images.

SynVisio requires two files to run:

  • The simplified gff file that was used as an input for a McScanX query.
  • The collinearity file generated as an output by McScanX for the same input query.
  • Optional track file in bedgraph format to annotate the generated charts.

SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.

Address of the bookmark: https://synvisio.github.io/#/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44571/panacus-a-counting-tool-for-pangenome-graphs Fri, 14 Jun 2024 14:42:28 -0500 https://bioinformaticsonline.com/bookmarks/view/44571/panacus-a-counting-tool-for-pangenome-graphs <![CDATA[Panacus : A Counting Tool for Pangenome Graphs]]> panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.

panacus supports the following calculations:

  • coverage histogram
  • pangenome growth statistics
  • path-/group-resolved coverage table

Address of the bookmark: https://github.com/marschall-lab/panacus

]]> Neel