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- Neel@neelam
Neel published a news post Submit your SARS-CoV-2 sequence data to GenBank 1689 days ago

Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page.
- BioStar@biostar
BioStar bookmarked Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes. 1689 days ago

Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly,...

https://github.com/dahak-metagenomics/dahak
- BioStar@biostar
BioStar posted to the wire 1692 days ago

IIT Delhi invites proposals for supercomputer-based COVID-19 research; Offers Rs 1 crore worth of computational time for FREE http://supercomputing.iitd.ac.in/ #IIT #Delhi #COVID #Free #SuperComputer
- Rahul Nayak@rahul
Rahul Nayak posted to the wire 1693 days ago

Extract the underscore separated values. $ awk '{split($0,a,"_"); print a[1]"_"a[2]}' aaa.txt | sort | uniq -u > all_ids_sm.txt #awk #bash #underscore #list
- BioStar@biostar
BioStar commented on the blog List of gene ontology software and tools 1694 days ago

GeneSCF serves as command line tool for clustering list of genes based on functional annotation (Geneontology, KEGG, REACTOME and NCG). This tool requires gene list in the form of Entrez Gene IDs or Official gene symbols as a...
- BioStar@biostar
BioStar commented on the blog List of gene ontology software and tools 1694 days ago

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;128(14). http://amp.pharm.mssm.edu/Enrichr/
- Rahul Nayak@rahul
Rahul Nayak posted to the wire 1696 days ago

Basics commands for Docker https://www.digitalocean.com/community/tutorials/how-to-remove-docker-images-containers-and-volumes #Docker #commands
- Neel@neelam
Neel bookmarked QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses. 1697 days ago

Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBank and STITCH. These data usually reflect observed interactions, while the lack of data for a given protein-drug/chemical pair...

http://quartata.csb.pitt.edu/
- BioStar@biostar
BioStar bookmarked HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from... 1701 days ago

HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...

https://github.com/marbl/canu
- Rahul Nayak@rahul
Rahul Nayak published a blog post New Machine Learning Packages in R 1702 days ago

Machine Learning
- Neel@neelam
Neel bookmarked Coronavirus Resources ! 1704 days ago

2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific...

https://bigd.big.ac.cn/ncov/about
Comments
- Surabhi Chaudhary@surabhi
  
  Surabhi Chaudhary 1245 days ago
  Some important resources here https://artic.network/ncov-2019
- LEGE@lege
  
  LEGE 1163 days ago
  Illumina toolkit for SARS-CoV2
  https://sapac.illumina.com/informatics/biological-interpretation/coronavirus-software.html#about
- LEGE@lege
  
  LEGE 1163 days ago
  
  The US government SARS-CoV-2 Interagency Group (SIG) developed a Variant Classification scheme that defines three classes of SARS-CoV-2 variants:
  
  Variant of Interest
  
  Variant of Concern
  
  Variant of High Consequence
  
  Intersting piece of information
  https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html
+12 more
- Neel@neelam
Neel posted to the wire 1704 days ago

https://covid-19.dnastack.com/_/discovery?position=3840&referenceBases=A&alternateBases=G #COVID-19 #Beacon #COVID #Share #Data
- Jit@jit.aber
Jit bookmarked tinycov: standalone command line utility written in python to plot coverage from a BAM file 1706 days ago

Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter. To install the stable version: pip3 install --user...

https://github.com/cmdoret/tinycov
- Jit@jit.aber
Jit bookmarked chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps 1706 days ago

Python package to detect chromatin loops (and other patterns) in Hi-C contact maps. Stable version with pip: pip3 install --user chromosight Stable version with conda: conda install -c bioconda -c conda-forge chromosight or, if you want...

https://github.com/koszullab/Chromosight
- Shruti Paniwala@shruti
Shruti Paniwala bookmarked Magic-BLAST 1709 days ago

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...

https://ncbi.github.io/magicblast/
- Radha Agarkar@radhaagarkar
Radha Agarkar created a new bio-script Check os version in Linux ! 1709 days ago
- Jit@jit.aber
Jit posted to the wire 1709 days ago

MyBib is a nice alternative for bibliography https://www.mybib.com/ #MyBib #Citation #Referencing
- Jit@jit.aber
Jit bookmarked ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis 1711 days ago

ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements. ProteoClade helps you analyze two...

https://github.com/HeldLab/ProteoClade
- Jit@jit.aber
Jit posted to the wire 1711 days ago

As of 2020-03-11, 445 strains of virus have been sampled, with a total of 285 haplotypes. #nCov #Corona
- Jit@jit.aber
Jit created a new bio-script Basic docker commands ! 1711 days ago
Comments
- Jit@jit.aber
  
  Jit 1174 days ago
  Attached the running docker
  Instead of using -i or -t options, use the attach command to connect to a running container:
  docker attach container_id
- Jit@jit.aber
  
  Jit 1174 days ago
  Start the docker container
  docker start [options] container_id
  Stop the docker container
  docker stop --time=20 container_id
  Kill a docker container
  docker kill [option] container_id

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