BOL: Related items

Single Cell RNAseq data analysis tutorial !!

Robert M Willioms — Mon, 27 Nov 2017 16:24:29 -0600

A major breakthrough (replaced microarrays) in the late 00’s and has been widely used since
Measures the average expression level for each gene across a large population of input cells
Useful for comparative transcriptomics, e.g. samples of the same tissue from different species
Useful for quantifying expression signatures from ensembles, e.g. in disease studies
Insufficient for studying heterogeneous systems, e.g. early development studies, complex tissues (brain)
Does not provide insights into the stochastic nature of gene expression

Following are the useful links:

Single Cell RNAseq data analysis Tutorial

A step-by-step workflow for low-level analysis of single-cell RNA-seq data

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

SCell: single-cell RNA-seq analysis software

https://github.com/diazlab/SCell

Beta-Poisson model for single-cell RNA-seq data analyses

https://github.com/nghiavtr/BPSC

Sincera: A Computational Pipeline for Single Cell RNA-Seq Profiling Analysis

https://research.cchmc.org/pbge/sincera.html

SC3 – consensus clustering of single-cell RNA-Seq data

http://biorxiv.org/content/early/2016/09/02/036558

Citrus: A toolkit for single cell sequencing analysis

http://biorxiv.org/content/early/2016/09/14/045070

Single-Cell Resolution of Temporal Gene Expression during Heart Development

http://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30682-7

Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects

http://biorxiv.org/content/early/2016/11/15/087775

Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes

http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract

SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

http://biorxiv.org/content/early/2016/11/21/088856

SCOUP is a probabilistic model to analyze single-cell expression data during differentiation

https://github.com/hmatsu1226/SCOUP

scLVM is a modelling framework for single-cell RNA-seq data

https://github.com/PMBio/scLVM

Selective Locally linear Inference of Cellular Expression Relationships (SLICER) algorithm for inferring cell trajectories

https://github.com/jw156605/SLICER

SinQC: A Method and Tool to Control Single-cell RNA-seq Data Quality

http://www.morgridge.net/SinQC.html

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

https://github.com/zji90/TSCAN

Visualization and cellular hierarchy inference of single-cell data using SPADE

http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html

OEFinder: Identify ordering effect genes in single cell RNA-seq data

https://github.com/lengning/OEFinder

Traineeship at JAWAHARLAL NEHRU TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE

Fri, 25 Nov 2016 08:07:59 -0600

JAWAHARLAL NEHRU TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE

THIRUVANANTHAPURAM - 695 562

Traineeship on Bioinformatics(2)

First class M.Sc. Bioinformatics/ Agriculture/ Botany/ Biotechnology @ Rs.8000

Those candidates who fulfill the above criteria may attend a walk PCC Coordinator in-interview on 28th November 2016 at Saraswathy Thangavelu center, JNTBGRI, Puthenthope, Thiruvananthapuram between at 10.00 am and 2.00 pm with all the relevant document and testimonials.

No TA/DA will be given to candidates for attending the interview.

More Info : http://jntbgri.res.in/downloads/traineeship_notification.pdf

Research Associate and Junior Research Fellow at North-Eastern Hill University - Tura, Meghalaya

Fri, 28 Oct 2016 09:54:43 -0500

Research Associate and Junior Research Fellow
North-Eastern Hill University - Tura, Meghalaya
₹18,000 a month
Applications are invited for the post of Research Associate and JRF in the DBT sponsored Bioinformatics Infrastructure Facility (BIF), posts are purely temporary and terminable at anytime without prior notice or assigning any reason thereof.

Research Associate :
Essential Qualification: Ph.D in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.36000-/- + Admissible 10% HRA per month
Age: Below 35 years

Junior Research Fellow
Essential Qualification: M.Sc in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.18000-/- + per month
Age: Below 35 years

Last date for receving application by mail or post is 08.11.2016

Company Info.
North-Eastern Hill University

Bioinformatics Infrastructure Facility (BIF) Department of RDAP North-Eastern Hill University, Tura Campus Tura-794002, Meghalaya

More at http://www.nehu.ac.in/Advertisements/BIFTuraManpowerAdvt_25102016.pdf

DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Jit — Sat, 25 Jan 2020 13:28:09 -0600

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the TensorFlow machine learning framework.

https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html

https://www.biorxiv.org/content/10.1101/092890v6

Address of the bookmark: https://github.com/google/deepvariant

Information Officer at IIAR, Gujarat

Fri, 04 Nov 2016 05:19:13 -0500

Walk in interview at 10.30 am on Nov 11th, 2016 for the following position at Distributed Information Sub-Centre (DISC) established by Dept. Of Biotechnology, Govt. of India at Indian Institute of Advanced Research, Gandhinagar, Gujarat

Position (scale), qualifications and experience

1. Information Officer (Rs 8000-275-13500): one post
Qualifications and experience: MCA, Post-Graduate in any field of biosciences, bioinformatics with at least two years of experience in working in a bioinformatics setup and good knowledge of linux operating system and computer networking.

General terms and conditions:
1. The above engagements is presently till March 31st, 2017. However on extension of project grant and satisfactory performance of the candidate, your services can be extended beyond March 31st, 2017 based on the terms and conditions of extension of project grant.

2. It is not an appointment with the institute and will not confer any right to the incumbent to any claim implicit or explicit on any position.

3.No TA/DA will be paid for attending the interview. Outstation candidates have to make their own arrangement for their stay.

4.Candidates, appearing in the walk-in interview are requested to bring the hard copy of application addressed to Dr. Anju Pappachan with latest photograph, CV mentioning qualifications, work experience and name of two referees and one page write up as to why you would like to join the project.

Address:
Dr. Anju Pappachan
Indian Institute of Advanced Research (IIAR),
University and Institute of Advanced Research,
The Puri Foundation for Education in India,
Koba Institutional Area,
Gandhinagar- 382 007, Gujarat, India. Contact no. 079-30514152
e-mail- anju@iiar.res.in

Juicebox: Visualization and analysis software for Hi-C data

Jit — Fri, 21 Feb 2020 00:33:38 -0600

Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.

Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly.

GUI at https://aidenlab.org/juicebox/

Address of the bookmark: https://github.com/aidenlab/Juicebox

RA Bioinformatics at NATIONAL INSTITUTE OF CANCER PREVENTION & RESEARCH (ICMR)

Thu, 17 Nov 2016 04:11:09 -0600

NATIONAL INSTITUTE OF CANCER PREVENTION & RESEARCH (ICMR)

Noida 201301 (U.P)

Applications are invited upto 21.11.2016 from interested candidates as per details available on NICPR website (www.nicpr.res.in)/ ICMR website (www.icmr.nic.in) to fill up following temporary position in the time bound DHR Project entitled “Next generation EGFR inhibitor identification using ligand based QSAR technique” under Dr. Subhash M. Agarwal, Scientist-D, Division of Bioinformatics.

Research Assistant (One)

Rs.27000/- p.m. (Fixed/temporary)

Essential: M.Sc. in Bioinformatics or related field.

Desirable: Experience in QSAR and structure based drug designing.

More Info : www.icmr.nic.in/icmrnews/NICPR_Advertisement%20for%20RA.pdf

wgd—simple command line tools for the analysis of ancient whole-genome duplications

LEGE — Thu, 23 Jul 2020 05:49:45 -0500

wgd is a easy to use command-line tool for K_S distribution construction named wgd. The wgd suite provides commonly used K_S and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.

https://academic.oup.com/bioinformatics/article/35/12/2153/5162749

Address of the bookmark: https://github.com/arzwa/wgd

Professor (all levels) in Bioinformatics and Computational Biology

Tue, 22 Nov 2016 05:43:38 -0600

King Abdullah University of Science and Technology (KAUST) (kaust.edu.sa) is seeking a highly motivated and skilled faculty member for the Bioinformatics track whose research focuses on development of methods and tools for Bioinformatics and Computational Biology.
KAUST is an international, graduate-level research university dedicated to advancing science and technology through interdisciplinary research, education, and innovation. Located on the shores of the Red Sea in Saudi Arabia, KAUST offers superb research facilities, generous assured research funding, and internationally competitive salaries, attracting top international faculty, scientists, engineers, and students to conduct fundamental and goal-oriented research to address the world’s pressing scientific and technological challenges in the areas of food, water, energy, and the environment.
The successful applicant is expected to develop world-leading research in domain of bioinformatics/computational biology with focus on development of novel computational approaches for efficient and accurate methods of analyzing biological phenomena at molecular level. The faculty member will be part of the Computational Bioscience Research Center (CBRC) within the Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division. The position will remain open until filled.

Requirements:

PhD or equivalent in a Computer Science, Mathematics or Engineering discipline. Candidates should be well-established within the research field relevant to the position grade. They should demonstrate original research and experience at the highest international level.

Responsibilities and tasks:

Research competence in the following areas is preferred:
Analysis of next generation sequencing (NGS) and other ‘omics’ data (e.g. CAGE, ChIP-Seq, DHS, RNA-Seq, Ribo-Seq, proteomic, metabolic and NMR spectra, etc.).
Signaling, regulatory and metabolic pathways analysis.
Development of tools (web-based and standalone) suited for efficient computational biology/bioinformatics.

Visit cemse.kaust.edu.sa to apply.

Kmer: a suite of tools for DNA sequence analysis

BioStar — Wed, 18 Aug 2021 00:02:54 -0500

More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

A2Amapper: ATAC, Assembly to Assembly Comparision tool:
- Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).

Sim4db:
- Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.

LEAFF:
- LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

Meryl:
- An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer