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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (169 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (626 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (787 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 (839 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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gggenomes: A grammar of graphics for comparative genomics
By Surabhi Chaudhary 1392 days agogithub.com - gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization packageggplot2 by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example,...flutter
By Neel 1396 days agohttps://flutter.dev/ - Flutter is Google’s UI toolkit for building beautiful, natively compiled applications for mobile, web, and desktop from a single codebase.Introduction to Bioinformatics and Computational Biology
By Jit 1400 days agoliulab-dfci.github.io - This is the course material for STAT115/215 BIO/BST282 at Harvard University. Xiaole Shirley Liu (lead instructor)Joshua StarmerMartin HembergTing WangFeng Yue Ming TangYang LiuJack KangScarlett GeJiazhen RongPhillip NicolMaartin De Vries We...3D Genome Browser: explore chromatin interaction data, such as Hi-C, ChIA-PET, Capture Hi-C,...
By BioStar 1402 days ago3dgenome.fsm.northwestern.edu - Beside visualizing chromatin interaction data, you can also seamlessly browse other omics data such as ChIP-Seq or RNA-Seq for the same genomic region, and gain a complete view of both regulatory landscape and 3D genome structure for any given gene....Pandoc: The universal markup converter
By Manisha Mishra 1407 days agogithub.com - Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. Pandoc is a free and open-source document converter, widely used as a writing tool and as a basis for...MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Manisha Mishra 1407 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...BUSCO datasets !
By Jit 1411 days agobusco-data.ezlab.org - The BUSCO software now directly downloads the necessary datasets, specified by the user or automatically selected. To display all available datasets busco --list-datasets You can also download them manually and see...MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic...
By Jit 1411 days agogithub.com - MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to...AutoGluon: AutoML for Text, Image, and Tabular Data
By Jit 1418 days agogithub.com - AutoGluon automates machine learning tasks enabling you to easily achieve strong predictive performance in your applications. With just a few lines of code, you can train and deploy high-accuracy machine learning and deep learning models on text,...The Breeding API (BrAPI) project
By BioStar 1418 days agohttps://brapi.org/ - The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases. BrAPI is a standardized RESTful web service API specification for communicating plant breeding data. This community driven standard is free to...
