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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (203 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (660 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (821 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (873 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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genomics public data links !
By Jit 1781 days agoconsole.cloud.google.com - 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/netGO: R-Shiny package for network-integrated pathway enrichment analysis
By Jit 1782 days agogithub.com - 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...Sequanix: a dynamic graphical interface for Snakemake workflows
By BioStar 1782 days agogithub.com - 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...Biological databases !
By BioStar 1782 days ago Comments (4)ftp.ncbi.nih.gov - 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.htmljtools : more efficient presentation of regression analyses
By Neel 1782 days agocran.r-project.org - 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...cisMuton: caller that detects SNVs/indels by comparing target (foreground) and control (background)...
By Jit 1783 days agostatic.ciscall.org - 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...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Jit 1784 days agogithub.com - Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike...Leaflet: JavaScript libraries for interactive maps
By Jit 1784 days agorstudio.github.io - Leaflet is one of the most popular open-source JavaScript libraries for interactive maps. Features Interactive panning/zooming Compose maps using arbitrary combinations of: Map...PANEV: an R package for a pathway-based network visualization
By Jit 1785 days agogithub.com - PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to n) of interconnected upstream and...Bioinformatics related group
By Rahul Agarwal 1785 days agobioinformatik.de - FaBI emerged from the respective groups of the four founding societies GI (German Informatics Society), DECHEMA (Society for Chemical Engineering and Biotechnology), GBM (Society for Biochemistry and Molecular Biology) and GDCh (German Chemical...
