<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/2728?offset=1210 https://bioinformaticsonline.com/bookmarks/view/37749/d2tools-the-toolbox-for-counting-the-frequency-of-k-tuple-from-sequencing-datasets-and-calculate-the-dissimilarity Thu, 20 Sep 2018 08:38:29 -0500 https://bioinformaticsonline.com/bookmarks/view/37749/d2tools-the-toolbox-for-counting-the-frequency-of-k-tuple-from-sequencing-datasets-and-calculate-the-dissimilarity <![CDATA[d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate the dissimilarity]]> d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style(d2/d2*/d2S representing d2/d2Star/d2shepp, respectively) measures. Hao, Dai, Eucliean, Mahattan, and Chebyshev distance measures are also included in d2Tools.

Manual at https://code.google.com/archive/p/d2-tools/wikis/d2ToolMannual.wiki

Address of the bookmark: https://code.google.com/archive/p/d2-tools/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38205/sim3c-read-pair-simulation-of-3c-based-sequencing-methodologies-hic-meta3c-dnase-hic Tue, 13 Nov 2018 07:25:38 -0600 https://bioinformaticsonline.com/bookmarks/view/38205/sim3c-read-pair-simulation-of-3c-based-sequencing-methodologies-hic-meta3c-dnase-hic <![CDATA[sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)]]> Required python modules

  • biopython
  • intervaltree
  • numpy
  • scipy
  • tqdm
  • PyYAML

Address of the bookmark: https://github.com/cerebis/sim3C

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data Tue, 22 Jan 2019 06:26:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data <![CDATA[Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data]]>
  • Run a pipeline processing fast5s to a consensus in a single command.
  • Recommended fixed "standard" and "fast" pipelines.
  • Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
  • Seemless distribution of tasks over local or distributed compute.
  • Highly configurable.
  • Open source (Mozilla Public License 2.0).

    • Documentation can be found at https://nanoporetech.github.io/katuali/.

    Address of the bookmark: https://github.com/nanoporetech/katuali

    ]]>     Jit     https://bioinformaticsonline.com/researchlabs/view/39827/prof-dr-med-andreas-ramming Wed, 07 Aug 2019 03:25:48 -0500 <![CDATA[Prof. Dr. med. Andreas Ramming]]> In many autoimmune diseases, a misdirected immune response leads to chronic inflammation and subsequently to fibrotic and degenerative tissue remodeling. Therapeutic options are available for inflammatory joint diseases, but only about 40% of patients respond to these existing therapies on a permanent basis. In the remaining cases, these therapies miss their target from the beginning or later during the course of treatment failure. There are currently no causal therapies available for the treatment of fibrotic autoimmune diseases such as systemic sclerosis. Therefore, there is an urgent need to develop new therapeutic options for the treatment of fibrotic and synovitic autoimmune diseases. His group is therefore deal with the molecular mechanisms of these misdirected signaling pathways for the development of novel, targeted therapies

    http://www.medizin3.uk-erlangen.de/forschung/arbeitsgruppen/matrixbiologie-entzuendliche-signalwege-in-arthritis-und-fibrose/

    ]]>         https://bioinformaticsonline.com/opportunity/view/21472/asst-professor-at-central-university-of-jharkhand-cuj Sun, 01 Mar 2015 01:17:52 -0600 <![CDATA[Asst. Professor at Central University of Jharkhand (CUJ)]]> Central University of Jharkhand (CUJ) has issued a recruitment notification for the recruitment of Assistant Professor through recruitment notification – Central University of Jharkhand (CUJ) Recruitment 2015 – Advt. No.: CUJ/Advt./14-15/15 Date: 26th Feb. 2015. Candidates who have completed M.Sc, Ph.D can apply for the new recruitment notification from Central University of Jharkhand (CUJ)

    Central University of Jharkhand has been granted funds by the Department of Biotechnology (DBT), Govt. of India to establish “DBT-Boost to CUJ Interdisciplinary Life Sciences Departments for Education and Research” Applications are invited for the Assistant Professor on purely temporary basis. The appointments shall be initially for a period of one year, renewable every year depending on the satisfactory performance, till the end of project.

    Position: ASSISTANT PROFESSOR (Total 03)
    Salary: 45,000/- (fixed) per month
    Essential Qualifications: i. Good academic record with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the master’s degree level with specialization in Biodiversity and Systematic/ Systems Biology/ Biophysics/ Bioinformatics from an Indian University, or an equivalent degree from an accredited foreign university. ii. Besides fulfilling the above qualifications, the candidates must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/SET. iii. Notwithstanding anything contained in i. and ii. candidates, who are or have been awarded Ph.D Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulation, 2009, shall be exempted from therequirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor. iv. NET/SLET/SET shall also not be required for such disciplines for which NET/SLET/SET in not conducted.
    Desirable: Preference will be given to candidates having Ph.D in any of the above mentioned areas with NET

    IMPORTANT DATES TO REMEMBER :

    Last Date to Apply for this job 24/3/2015

    REFERENCE:

    Central University of Jharkhand (CUJ) Recruitment 2015 – Advt. No.: CUJ/Advt./14-15/15 Date: 26th Feb. 2015.

    More at http://cuj.ac.in/careers.php

    ]]>         https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data Sat, 25 Jan 2020 13:28:09 -0600 https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data <![CDATA[DeepVariant : 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 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

    image

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

    ]]>     Jit     https://bioinformaticsonline.com/opportunity/view/21624/ra-bioinformatics-at-ch-charan-singh-university-meerut Wed, 11 Mar 2015 09:07:07 -0500 <![CDATA[RA Bioinformatics at Ch. Charan Singh University, Meerut]]> Ch. Charan Singh University, Meerut

    http://molbiolabccsumrt.webs.com/

    Applications are invited for one post of RA in a DBT funded research project “Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) Scheme of BTISet”.

    Candidate should have a Ph.D. degree in Bioinformatics/Biotechnology/Genetics and Plant Breeding with adequate experience in the area of Bioinformatics. If a suitable candidate for the post of RA is not available, a JRF/SRF may be appointed.

    Candidate for the post of JRF/SRF should have Master’s degree in relevant subject with adequate experience in the area of Bioinformatics and should be NET/DBT-BINC qualified

    Interested candidates may send their bio-data to Prof. H. S. Balyan (hsbalyan@gmail.com) (in exceptional case, bio-data may also be submitted at the time of interview) and attend the interview on Monday, March 30, 2015 at 11:00 AM in the Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut. Candidates shall bring their original documents at the time of interview for verification. No interview letters will be issued and no TA/DA will be paid.

    ]]>         https://bioinformaticsonline.com/bookmarks/view/41046/iseqqc-a-tool-for-expression-based-quality-control-in-rna-sequencing Sun, 16 Feb 2020 08:47:17 -0600 https://bioinformaticsonline.com/bookmarks/view/41046/iseqqc-a-tool-for-expression-based-quality-control-in-rna-sequencing <![CDATA[iSeqQC: a tool for expression-based quality control in RNA sequencing]]> iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers.

    http://cancerwebpa.jefferson.edu/iSeqQC/

    https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3399-8

    Address of the bookmark: https://github.com/gkumar09/iSeqQC

    ]]>     BioStar     https://bioinformaticsonline.com/bookmarks/view/21703/coding-ground Tue, 17 Mar 2015 00:47:20 -0500 https://bioinformaticsonline.com/bookmarks/view/21703/coding-ground <![CDATA[Coding Ground]]> Online coding group for most of the programming languages.

    Code in almost all popular languages using Coding Ground. Edit, compile, execute and share your projects, 100% cloud.

    http://www.tutorialspoint.com/codingground.htm

    Address of the bookmark: http://www.tutorialspoint.com/codingground.htm

    ]]>     Jitendra Narayan     https://bioinformaticsonline.com/bookmarks/view/42485/fastprongs-fast-preprocessing-of-next-generation-sequencing-reads Sat, 26 Dec 2020 08:35:21 -0600 https://bioinformaticsonline.com/bookmarks/view/42485/fastprongs-fast-preprocessing-of-next-generation-sequencing-reads <![CDATA[FastProNGS: fast preprocessing of next-generation sequencing reads]]> FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. 

    Address of the bookmark: https://github.com/Megagenomics/FastProNGS

    ]]>     Rahul Nayak