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Latest activity

• • BioStar@biostar

  

  BioStar posted a new ad in the Opportunity Academic Posts at the University of Edinburgh 1790 days ago
• • Rahul Nayak@rahul

  

  Rahul Nayak created a new bio-script To convert just one specific read group to fastq 1791 days ago
• • Jit@jit.aber

  

  Jit commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 1791 days ago

  Current Protocols in Bioinformatics is a comprehensive source for protocols and reviews in the multidisciplinary field of bioinformatics, including the areas of analyzing expression patterns, pathway analysis, recognizing functional domains,...
• • Jit@jit.aber

  

  Jit bookmarked Cancer Dependency Map 1792 days ago

  The consequences of alterations in the DNA of cancer cells and subsequent vulnerabilities are not fully understood. This project aims to assign a dependency to every cancer cell in a patient which could be exploited to develop new therapies. This...

  https://depmap.sanger.ac.uk/
• • Jit@jit.aber

  

  Jit commented on a bookmark Biological databases ! 1792 days ago

  Chromosomes here https://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/
• • Jit@jit.aber

  

  Jit commented on a bookmark Biological databases ! 1792 days ago

  NCBI released a set of GATK-specific dbSNP VCF's, with the "chr" attached. Those can be accessed at ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.
• • Jit@jit.aber

  

  Jit commented on a bookmark Biological databases ! 1792 days ago

  List of useful biological databases at ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/
• • Jit@jit.aber

  

  Jit bookmarked genomics public data links ! 1792 days ago

  List of publically available databases on google server. More at https://software.broadinstitute.org/gatk/download/bundle ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/. ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

  https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1
• • Jit@jit.aber

  

  Jit bookmarked netGO: R-Shiny package for network-integrated pathway enrichment analysis 1792 days ago

  netGO is an R/Shiny package for network-integrated pathway enrichment analysis.netGO provides user-interactive visualization of enrichment analysis results and related networks. Currently, netGO supports analysis for four species...

  https://github.com/unistbig/netGO
• • BioStar@biostar

  

  BioStar answered the question Error: Could not find dictionary next to reference file file 1793 days ago

  Install Picard https://github.com/broadinstitute/picard/releases/tag/2.21.8 Then run following command: java -jar ../picard.jar CreateSequenceDictionary REFERENCE=GRCh38.primary_assembly.genome.fa...
• • Rahul Nayak@rahul

  

  Rahul Nayak asked Error: Could not find dictionary next to reference file file 1793 days ago

  htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///data/sata_data/workshop/wsu29/Parivartan/snakemake_germline_legacy/references/GRCh38.primary_assembly.genome.fa
• • BioStar@biostar

  

  BioStar bookmarked Sequanix: a dynamic graphical interface for Snakemake workflows 1793 days ago

  A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats). A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable...

  https://github.com/sequana/sequana
• • BioStar@biostar

  

  BioStar bookmarked Biological databases ! 1793 days ago

  Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ... ftp://ftp.ncbi.nih.gov/genomes/ https://hgdownload.soe.ucsc.edu/downloads.html

  ftp://ftp.ncbi.nih.gov/genomes/

  Comments

  • • Jit@jit.aber

    

    Jit 1792 days ago

    NCBI released a set of GATK-specific dbSNP VCF's, with the "chr" attached. Those can be accessed at ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

  • • Jit@jit.aber

    

    Jit 1792 days ago

    Chromosomes here https://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/

  • • Rahul Nayak@rahul

    

    Rahul Nayak 1787 days ago

    all GATK bundle at ftp://ftp.broadinstitute.org/bundle/hg38/

  +1 more
• • Neel@neelam

  

  Neel bookmarked jtools : more efficient presentation of regression analyses 1793 days ago

  This package consists of a series of functions created by the author (Jacob) to automate otherwise tedious research tasks. At this juncture, the unifying theme is the more efficient presentation of regression analyses. There are a number of...

  https://cran.r-project.org/web/packages/jtools/readme/README.html
• • Jit@jit.aber

  

  Jit posted to the wire 1793 days ago

  Ingenuity Pathway Analysis https://digitalinsights.qiagen.com/products-overview/analysis-and-visualization/qiagen-ipa/ #pathway #analysis #enrichment
• • Jit@jit.aber

  

  Jit bookmarked cisMuton: caller that detects SNVs/indels by comparing target (foreground) and control (background)... 1794 days ago

  cisMuton is a caller that detects SNVs/indels by comparing target (foreground) and control (background) samples. cisMuton calls mutations from target capture regions, which are defined by the overlapping regions...

  https://static.ciscall.org/cisCall5_doc/index.html
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 1794 days ago

  #Evolutionary Dynamics of #microRNA target sites across #vertebrate #evolution https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008285
• • Rahul Nayak@rahul

  

  Rahul Nayak answered the question How to Calculate Illumina Read Length ? 1794 days ago

  Because one base is sequenced per cycle, the total number of cycles indicates the maximum number of bases that can be sequenced. You can use sequencing reagents to generate single continuous reads or for paired-end sequencing in both directions....
• • Neel@neelam

  

  Neel asked How to Calculate Illumina Read Length ? 1794 days ago

  Hi, I wanted to know how to calculate illumina read length 
• • Rahul Nayak@rahul

  

  Rahul Nayak created a new bio-script Update conda ! 1795 days ago

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