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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (310 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (767 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (928 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 (980 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Cancer Dependency Map
By Jit 1888 days agodepmap.sanger.ac.uk - 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...genomics public data links !
By Jit 1888 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 1888 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 1889 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 1889 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 1889 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 1890 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 1891 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 1891 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 1891 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...
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