BOL: Related items

BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks

Rahul Nayak — Sun, 20 Dec 2020 11:43:45 -0600

With BioJupies you can produce in seconds a customized, reusable, and interactive report from your own raw or processed RNA-seq data through a simple user interface

BioJupies now supports user accounts! Sign in from the top right corner of the page for access to unlimited private notebooks, RNA-seq datasets and alignment jobs.

Address of the bookmark: https://amp.pharm.mssm.edu/biojupies/

ICAR project RA position @ Institute of Bioinformatics (IOB) Bangalore

Tue, 22 Sep 2015 23:41:31 -0500

Applications are invited for the post of Research Associate (RA) in the ICAR project on "Lactation stress associated postpartum anestrus SNP array in buffaloes". We are looking for a motivated candidate for handling Next Generation sequencing data analysis with a strong background in bioinformatics and programming.

The position is open for immediate appointment and available for two years and then extendable for additional one year. The applicant will be appointed as Research Associate based on qualifications as detailed below:

Research Associate:

-Master’s degree with bioinformatics with at least 2 years of research experience in Next Generation sequencing data analysis as evidence from Fellowship/ Associateship / Training / other engagements.

-Familiarity with bioinformatics tools, database development, programming skills

-Minimum 1 publication in any peer reviewed journal

Salary will be as per ICAR rules and guidelines. Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.

Interested candidates may send a Letter of Interest and CV by email to: keshav@ibioinformatics.org before September 29, 2015.

RNA-seq workflow: gene-level exploratory analysis and differential expression

Jit — Sat, 09 Oct 2021 07:59:23 -0500

Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count datasets for downstream analysis. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.

Address of the bookmark: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

Pathway Analysis

Rahul Agarwal — Fri, 03 Oct 2014 08:51:13 -0500

Pathway Analysis is usually performed with aim to enrich the genes with their functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particular set of expressed genes follow but also to disclose the relationships between these genes. With availability of more genomics, transcriptomics and proteomics data, interactions between genes involve in multiple pathways become more clear and also relationships between the genes, their transcripts, and their gene products. However, existing tools and dbs mainly based on knowledge driven approach in which pathways will be identified by finding the correlation between the information in one of the pathway knowledge databases (KEGG,Reactome,Panther,BioCarta, Panther,GO,NCI,WikiPathways,etc) and gene expression result for a specific conditions for instance tumor, obesity , cold resistant crops/plants, etc.

Introductory Articles/ppt/sources:

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002375

http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures09/Pathway%20Analysis.pdf

http://gettinggeneticsdone.blogspot.de/2012/03/pathway-analysis-for-high-throughput.html

http://davetang.org/muse/tag/pathway/

https://www.biostars.org/p/42219/

http://bioinformatics.ca//files/public/Pathways_2014_Module4_v2.pdf

http://bioinformatics.ca//files/public/Pathways_2014_Module2.pdf

Impotant Database and Tools:

GeneMANIA, Cytoscape, IPA and Metacore (Commerical ), Pathway Commons, Reactome ,Panther, BioCyc, WikiPathways, Pathvisio, KEGG, NCI, Stringdb, Amigo, WebGestalt ,ConsensusPathDB ,GSEA,Blast2go

Popular R based tools:

Reactome.db, ReactomePA, ClusterProfiler, Gage, SPIA, topGO, Pathview,DOSE,GOStat

More:

http://www.bioconductor.org/help/search/index.html?q=Enrichment+analysis+

Webinar on Unique Molecular Identifier (UMI)-powered Ultra-sensitive Variant Calling using Strand NGS - Case Study

Strand — Tue, 07 Nov 2017 03:55:52 -0600

Webinar on Unique Molecular Identifier-powered Ultra-sensitive Variant Calling using Strand NGS - Case Study

by Dr. Pandurang Kolekar, Bioinformatics Engineer, Strand Life Sciences

Abstract:

Unique Molecular Identifiers (UMIs) are short random nucleotide sequences that are increasingly being used in high-throughput sequencing experiments. In this webinar, we will highlight the UMI-friendly features of Strand NGS v3.1 including support for handling well known and customised UMI libraries, QC metrics, consensus alignment, UMI-based family size filters for read list, genome browser enabled with UMI-specific features and filters, UMI-aware variant calling parameters, and exporting UMI-tagged aligned samples. These all features together empower users to harness the potential of UMI-tagged NGS data for deeper insights. A case study demonstrating application of these UMI-based features in Strand NGS for low frequency variant calling in cfDNA sample will be presented.

UMI-tagged NGS libraries allow, ultra-sensitive detection of low frequency variants from liquid biopsy samples using DNA-Seq and accurate quantification of transcript-level expression using RNA-Seq. The recent release of Strand NGS v3.1, is equipped with the necessary features to efficiently analyse UMI-tagged NGS data helping researchers and labs involved in rare variant calling like in cfDNA based cancer diagnostics, and accurate transcript quantification with RNA-Seq.

Webinar Details:

Session 1: 13 Dec 2017, 2:30 PM IST
Session 2: 13 Dec 2017, 9:30 PM IST

Register here: http://www.strand-ngs.com/webinar_registration

Project Fellow at Indian Institute of Chemical Biology (IICB)

Tue, 22 Sep 2015 23:47:35 -0500

Advertisement No. : R&C/CD/427/2015 ,Vacancy Code: 4271501

Project Fellow Bioinformatics recruitment in Indian Institute of Chemical Biology (IICB) purely temporary

Name of the Project: "Genomics and Informatics Solutions for Integrating Biology(Genesis)".

No. of Vacancies: 1

Qualification required : M.Sc in Bioinformatics with 55% Marks.

Experience (Desirable): Candidate should be well versed with sequencing data analysis,assembly and annotation of whole genome sequence. Experience in transcriptional data analysis is also preferred.

Age Limit : 28 Years

Stipend : Rs.16000
How to apply
Interested candidates may appear for the walk-in-interview to be held on 28.09.2015 from 11.00 a.m. in the Red Carpet Room with the following documents self attested copy - (1) Matriculation Certificate in support of your date of birth, (2) Degree/Diploma Certificate, (3) Original reprints of all testimonials regarding educational qualification, (4) No Objection Certificate from the employer if employed, (5) Final Mark Sheet of M.Sc. Examination, (6) One Passport size photograph.

http://www.career.iicb.res.in/Recruitment%20Notice.php

RNA-Seq differential expression work flow using DESeq2

BioStar — Mon, 23 Aug 2021 10:57:14 -0500

One of the aim of RNAseq data analysis is the detection of differentially expressed genes. The package DESeq2 provides methods to test for differential expression analysis.

Address of the bookmark: http://www.sthda.com/english/wiki/rna-seq-differential-expression-work-flow-using-deseq2

dupRadar package

Jit — Sun, 04 Feb 2018 14:28:57 -0600

The dupRadar package gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it. Thus, failed experiments can be easily identified at a glance

Address of the bookmark: https://bioconductor.org/packages/3.7/bioc/vignettes/dupRadar/inst/doc/dupRadar.html

LAST

Archana Malhotra — Wed, 09 Mar 2016 14:27:01 -0600

LAST can:

Handle big sequence data, e.g:
- Compare two vertebrate genomes
- Align billions of DNA reads to a genome
Indicate the reliability of each aligned column.
Use sequence quality data properly.
Compare DNA to proteins, with frameshifts.
Compare PSSMs to sequences
Calculate the likelihood of chance similarities between random sequences.
Do split and spliced alignment.
Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)

Sun, 20 Dec 2015 06:03:43 -0600

Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)
Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Mathematics / Applied Mathematics, Stati, Zoology)
Location : Kolkata
Last Date : 31 Dec 2015
Hiring Process : Written-test

NO: 340/ESTB/ADMN/NIBMG/2015-16
Doctoral Research In Biomedical Genomics, Including Statistical Genomics conduct National Institute of Biomedical Genomics (NIBMG)
Information For Students Interested To Pursue Doctoral Research In Biomedical Genomics, Including Statistical Genomics, At The National Institute Of Biomedical Genomics (Nibmg), Kalyan
Eligibility conditions for specific areas of research are :
Statistical Genomics : An applicant who wishes to pursue research in Statistical Genomics should hold a Master's degree (First class or equivalent) in a relevant discipline (Statistics, Mathematics, Bioinformatics, or a related discipline)
Biomedical Genomics : An applicant who wishes to pursue research in any area of biomedical genomics, other than statistical genomics, should hold a Master's degree (First class or equivalent) in a relevant discipline (Biochemistry, Biotechnology, Molecular Biology, Genetics, Zoology, Physiology, or a related discipline)
Fellowship : An applicant should have passed the NET conducted by CSIR/UGC/ICMR/DBT within the past ONE year AND should have been awarded a valid Junior Research Fellowship from CSIR, UGC, ICMR, DBT (Category-I only), DST (INSPIRE), NBHM. Preference will be given to candidates with demonstrable research training in the form of summer training or short-term courses in established research laboratories in preparation for a research career in biomedical sciences
How to apply
Online application will be accepted until 5 PM of December 31, 2015. A formal interview of the short-listed candidates will be held on January 12, 2016

More at http://www.nibmg.ac.in/?q=Career%20Opportunities