BOL: Related items

MGERT: Mobile Genetic Elements Retrieving Tool

Neel — Sat, 18 May 2019 08:58:01 -0500

MGERT is a computational pipeline for easy retrieving of MGE's coding sequences of a particular family from genome assemblies. MGERT utilizes several established bioinformatic tools combined into single pipeline which hides different technical quirks from an inexperienced user.

Address of the bookmark: https://github.com/andrewgull/MGERT

Genomic Medicine - Bruce Korf (2014)

Tue, 24 Jun 2014 07:58:44 -0500

May 21, 2014 - Current Topics in Genome Analysis 2014 A lecture series covering contemporary areas in genomics and bioinformatics. More: http://www.genome.gov/COURSE2014

R Package for PCA Analysis

LEGE — Sun, 24 Mar 2024 20:06:24 -0500

An R package for performing principal component analysis (PCA) of genomics data. The package performs PCA, generates the publication-ready plots, and identifies population-specific outlier individuals. The package can be accessed on GitHub: https://github.com/Devashish13/PopulationStructure

Address of the bookmark: https://rpubs.com/Devashish13/PCAGenomics

Faculty Positions at Central University of Punjab

Mon, 07 Jul 2014 23:33:33 -0500

Faculty Positions: Rolling/Open Advertisement Advt.No: T-10 (2013)

Pay Scale: Pay Band Rs.15600-39100 with AGP of Rs.6,000/-

Essential Qualifications for Professors, Associate Professors, and Assistant Professors: As per “UGC REGULATIONS ON MINIMUM QUALIFICATIONS FOR APPOINTMENT OF TEACHERS AND OTHER ACADEMIC STAFF IN UNIVERSITIES AND COLLEGES AND MEASURES FOR THE MAINTENANCE OF STANDARDS IN HIGHER EDUCATION 2010“ and the 2nd Amendments to the regulation issued in June 2013.

For details: http://www.ugc.ac.in/oldpdf/regulations/revised_finalugcregulationfinal10.pdf http://www.ugc.ac.in/pdfnews/8539300_English.pdf and University rules.

Procedure to apply:

Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 500/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:

Registrar, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001

For more info visit: http://www.centralunipunjab.com/Teaching/Final%20Details-t10-2013.pdf, http://www.centralunipunjab.com/Teaching/Advertisement-t10-2013.jpg

Last Apply Date: 31 Dec 2014

Figeno: Tool for plotting sequencing data along genomic coordinates.

LEGE — Tue, 17 Sep 2024 02:28:15 -0500

Tool for plotting sequencing data along genomic coordinates.

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

Address of the bookmark: https://github.com/CompEpigen/figeno

Integrative Genomics Viewer (IGV) tutorial

Neel — Sat, 12 Jul 2014 15:16:23 -0500

The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.

http://www.broadinstitute.org/igv/

Address of the bookmark: https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial

DAVI: Deep learning-based tool for alignment and single nucleotide variant identification

Jit — Tue, 16 Mar 2021 05:41:33 -0500

DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species

https://iopscience.iop.org/article/10.1088/2632-2153/ab7e19/pdf

Address of the bookmark: https://github.com/gguptaiitd/NEAT

COSMOS, our workflow management system for NGS data

Jit — Wed, 23 Jul 2014 07:29:14 -0500

COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via Advance Access in Bioinformatics (Gafni et al. 2014). It is also available for download for non-commercial academic and research purposes at:

http://cosmos.hms.harvard.edu/.

Address of the bookmark: https://cosmos.hms.harvard.edu/

Perlbrew: admin-free perl installation management tool.

Jit — Wed, 12 Jul 2017 03:53:08 -0500

perlbrew is an admin-free perl installation management tool. The latest version is 0.79, read the release note: Release 0.79.

Copy & Paste this line into your terminal:

\curl -L https://install.perlbrew.pl | bash

Or, if your system does not have curl but something else:

# Linux
\wget -O - https://install.perlbrew.pl | bash

# FreeBSD
\fetch -o- https://install.perlbrew.pl | sh

If you prefer to install with cpan, there are two steps:

sudo cpan App::perlbrew
perlbrew init

If it is installed with cpan, the perlbrew executable should be installed as /usr/bin/perlbrew or /usr/local/bin/perlbrew. For all users who want to use perlbrew, a prior perlbrew init needs to be executed.

The default perlbrew root directory is ~/perl5/perlbrew, which can be changed by setting PERLBREW_ROOTenvironment variable before the installation and initialization. For more advanced installation process, please read the perlbrew document.

Address of the bookmark: https://perlbrew.pl/

National Center for Bioinformatics (NCB)

Wed, 23 Jul 2014 14:10:49 -0500

NCB is offering M.Phil and Ph.D programs in the area of Bioinformatics. The major goal of NCB is to promote quality training and research in the area of Bioinformatics. Bioinformatics originated as a cross-disciplinary field as the need for computational sections to research problem raised in biomedicine.

More at http://ncb.qau.edu.pk/