BOL: Related items

mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Jit — Wed, 13 Nov 2019 22:20:19 -0600

mosdepth can output:

per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.
mean per-window depth given a window size--as would be used for CNV calling.
the mean per-region given a BED file of regions.
a distribution of proportion of bases covered at or above a given threshold for each chromosome and genome-wide.
quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20)
threshold output to indicate how many bases in each region are covered at the given thresholds.
A summary of mean depths per chromosome and within specified regions per chromosome.

Address of the bookmark: https://github.com/brentp/mosdepth

PhD position in Translational Medicine

Sat, 15 Feb 2020 06:07:19 -0600

https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/wissenschaftliche-r-mitarbeiter-in/phd-position-translational-medicine-129981.html?suid=1b510358c7578e8f75cf04a464fc21a404a574ca

Essential experience / qualifications:
Master / Diploma in Biology, Biochemistry, Molecular Medicine or similar; solid knowledge of molecular and cell biological techniques; good English knowledge

Applications:
Please send your application (including CV, letter of motivation, contact information of two references, and list of publication) by 13.03.2020 at the latest to:

Universitätsklinikum Erlangen
Chirurgische Klinik
Translational Research Center
Prof. Dr. rer. nat. Michael Stürzl
Schwabachanlage 12
91054 Erlangen
E-Mail: michael.stuerzl@uk-erlangen.de

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

Postdoctoral Researcher in Statistical Bioinformatics at Örebro University

Wed, 26 Aug 2020 10:20:11 -0500

The position is in Medical Sciences, with special focus on Statistical Bioinformatics.

The position is a full-time position for a fixed term of two years. The salary depends on the successful candidate’s qualifications and experience.

For more information, please contact Prof. Dirk Repsilber,This is an email address, Prof. Hugo Hesser, This is an email addressor Prof. Allan Sirsjö, allan.This is an email address, or Prof. Robert Brummer,This is an email address.

Örebro University actively pursues an equal work environment and values the qualities that diversity adds to our operations.

More detail at https://www.oru.se/english/working-at-orebro-university/jobs-and-vacancies/job/?jid=20200286/

Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome

BioStar — Wed, 22 Jul 2020 10:11:13 -0500

We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

More at https://pubmed.ncbi.nlm.nih.gov/20494974/

Address of the bookmark: http://www.sequenceontology.org/cgi-bin/soba.cgi

proActiv: Estimation of Promoter Activity from RNA-Seq data

BioStar — Thu, 13 Aug 2020 10:21:44 -0500

proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and provides absolute and relative promoter activity as output. The package can be used to identify active promoters and alternative promoters, the details of the method are described in Demircioglu et al.

Additional data on differential promoters in tissues and cancers from TCGA, ICGC, GTEx, and PCAWG can be downloaded here: https://jglab.org/data-and-software/

Address of the bookmark: https://github.com/GoekeLab/proActiv

Mobyle: a new full web bioinformatics framework

Jit — Sun, 07 Jan 2018 19:33:45 -0600

Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.

Address of the bookmark: https://academic.oup.com/bioinformatics/article/25/22/3005/179064

PilonGrid: parallel wrapper around the Pilon framework

Rahul Nayak — Thu, 13 Dec 2018 09:35:40 -0600

The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.

Address of the bookmark: https://github.com/skoren/PilonGrid

Dash: a web application framework that provides pure Python abstraction around HTML, CSS, and JavaScript.

Jit — Tue, 05 Nov 2019 06:39:48 -0600

Dash is a web application framework that provides pure Python abstraction around HTML, CSS, and JavaScript.

Dash Bio is a suite of bioinformatics components that make it simpler to analyze and visualize bioinformatics data and interact with them in a Dash application.

The source can be found on GitHub at plotly/dash-bio.

These docs are using Dash Bio version 0.1.4.

Address of the bookmark: https://dash.plot.ly/dash-bio

The Human Genome Project Video 3D Animation Introduction Low)

Sat, 24 Aug 2013 19:01:19 -0500