BOL: Related items

Lawley Lab

Mon, 09 May 2016 03:29:51 -0500

Lawley Lab are covered with a complex microbial community, known as our microbiota, which plays important roles in our physiology, immunity, metabolism and sustenance. Within the human gastrointestinal tract alone there are over 1,000 bacterial species, which amounts to approximately 10 times more cells than we harbor in our entire body and 200 times more genes than are found within our genome. Lawley Lab are really a 'supraorganism' consisting of our 'human' and 'microbial' selves.

More at http://www.sanger.ac.uk/science/groups/lawley-lab

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

BLOSUM50 Matrix

Radha Agarkar — Sat, 21 May 2016 22:12:15 -0500

BioGPS

Anjana — Mon, 23 May 2016 03:15:46 -0500

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

ClueGO

Jit — Thu, 02 Jun 2016 09:51:44 -0500

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/

methylKit

Jit — Fri, 03 Jun 2016 10:09:29 -0500

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

4DGenome

Jitendra Narayan — Mon, 04 Jul 2016 00:44:55 -0500

Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data cover both high throughput datasets and individiual focused studies.

All interaction data are freely available in a standardized file format. Records can be queried by genomic regions, gene names, organism, and detection technology.

Address of the bookmark: http://4dgenome.research.chop.edu/

Guest Faculty Centre for Bioinformatics at Pondicherry University

Wed, 15 Jun 2016 03:44:31 -0500

Guest Faculty Centre For Bioinformatics Jobs opportunity in Pondicherry University
Qualification : M.Phil. (with NET/SLET)/ M.Tech. / M.E. in Computer Science with a minimum of 55% of marks as per UGC norms.
Desirable : Ph.D and Teaching experience in Perl and Java programming.
Honorarium : Rs. 1,000/- per lecture (subject to a maximum of Rs. 25,000/- per month)
How to apply
Walk-in-Interview will be held on 29.06.2016 (Wednesday) at 2:30 P.M at the office of Centre for Bioinformatics, Pondicherry University, Puducherry — 605 014. Interested eligible candidates may attend the Walk-in-Interview along with all original certificates, self attested photocopies and testimonials with a copy of their bio-data. Candidates reporting after 2:30 P.M will not be entertained.

More at http://www.pondiuni.edu.in/news?quicktabs_2=5#quicktabs-2

clusterProfiler

Jit — Thu, 16 Jun 2016 18:57:03 -0500

statistical analysis and visulization of functional profiles for genes and gene clusters

Bioconductor version: Release (3.3)

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

Author: Guangchuang Yu with contributions from Li-Gen Wang and Giovanni Dall'Olio.

Maintainer: Guangchuang Yu

Citation (from within R, enter citation("clusterProfiler")):

Yu G, Wang L, Han Y and He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287.
Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("clusterProfiler")

https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

KisSplice

Jit — Tue, 16 Aug 2016 08:34:19 -0500

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.

KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely.

KisSplice comes as a workflow, with several possible post-treatments meant to facilitate the analysis of the results. The choice of the post-treatment depends on the availability of a reference genome/transcriptome and on the need to perform a differential analysis, as summarised in the following table.

Address of the bookmark: http://kissplice.prabi.fr/