BOL: Related items

BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks

Rahul Nayak — Sun, 20 Dec 2020 11:43:45 -0600

With BioJupies you can produce in seconds a customized, reusable, and interactive report from your own raw or processed RNA-seq data through a simple user interface

BioJupies now supports user accounts! Sign in from the top right corner of the page for access to unlimited private notebooks, RNA-seq datasets and alignment jobs.

Address of the bookmark: https://amp.pharm.mssm.edu/biojupies/

Fundamentals of Data Visualization by Claus O. Wilke

Abhi — Sat, 08 Jun 2024 16:07:19 -0500

The book is meant as a guide to making visualizations that accurately reflect the data, tell a story, and look professional. It has grown out of my experience of working with students and postdocs in my laboratory on thousands of data visualizations. Over the years, I have noticed that the same issues arise over and over. I have attempted to collect my accumulated knowledge from these interactions in the form of this book.

The entire book is written in R Markdown, using RStudio as my text editor and the bookdown package to turn a collection of markdown documents into a coherent whole. The book’s source code is hosted on GitHub, at https://github.com/clauswilke/dataviz.

Address of the bookmark: https://clauswilke.com/dataviz/

DAVI: Deep learning-based tool for alignment and single nucleotide variant identification

Jit — Tue, 16 Mar 2021 05:41:33 -0500

DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species

https://iopscience.iop.org/article/10.1088/2632-2153/ab7e19/pdf

Address of the bookmark: https://github.com/gguptaiitd/NEAT

bacLIFE: an automated genome mining tool for identification of lifestyle associated genes

BioStar — Fri, 15 Mar 2024 04:59:14 -0500

bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gene clusters associated with each lifestyle detected. This whole process is divided into different modules:

Clustering module Predicts, clusters and annotates the genes of every input genome
Lifestyle prediction Employs a machine learning model to forecast bacterial lifestyle or other specified metadata
Analitical module (Shiny app) Results from the previous modules are embedded in a user-friendly interface for comprehensive and interactive comparative genomics.

You can find the complete wiki here [https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki]

Address of the bookmark: https://github.com/Carrion-lab/bacLIFE

geNomad: Identification of mobile genetic elements

LEGE — Sun, 31 Aug 2025 06:40:17 -0500

geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.

Address of the bookmark: https://portal.nersc.gov/genomad

BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly

Jit — Mon, 22 May 2017 05:43:51 -0500

This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling. If you encounter any issues, please contact me at kklam@eecs.berkeley.edu. My name is Ka-Kit Lam.

https://github.com/kakitone/MetaFinisherSC

https://github.com/kakitone/BIGMAC

Address of the bookmark: https://github.com/kakitone/BIGMAC

sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets.

BioStar — Sat, 06 Jul 2024 04:24:06 -0500

sourmash is a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs for a variety of sequence comparisons. Some of our special sauce includes:

FracMinHash sketching, which enables accurate comparisons (including ANI) between data sets of different sizes
sourmash gather, a combinatorial k-mer approach for more accurate metagenomic profiling

Please see the sourmash publications for details.

The name is a riff off of Mash, combined with @ctb's love of whiskey. (Sour mash is used in making whiskey.)

Maintainers: C. Titus Brown (@ctb), Luiz C. Irber, Jr (@luizirber), and N. Tessa Pierce-Ward (@bluegenes).

sourmash was initially developed by the Lab for Data-Intensive Biology at the UC Davis School of Veterinary Medicine, and now includes contributions from the global research and developer community.

Address of the bookmark: https://github.com/sourmash-bio/sourmash

alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Jit — Mon, 12 Mar 2018 09:24:40 -0500

Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr

http://www.mdpi.com/2073-4425/8/10/248

Address of the bookmark: http://alienness.sophia.inra.fr/cgi/index.cgi

ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

Jit — Wed, 18 Mar 2020 14:27:20 -0500

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 general categories of experiments:

Targeted Database Searches: Experiments in which a limited number of species are defined ahead of time, such as those involving Patient-Derived Xenografts (PDXs) or host-pathogen interactions. Reference protein sequence databases are used for targeted searches (ex: using Mascot, MaxQuant).
De Novo Searches: Experiments in which the organisms are unspecified ahead of time or involve samples of high taxonomic complexity. Mass spectra are analyzed in the absence of a reference database (ex: using PEAKS, PepNovo).

ProteoClade scales from two organisms to every organism in UniProt. Please refer to the complete documentation at proteoclade.readthedocs.io for installation, a user's guide, and examples.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007741

Address of the bookmark: https://github.com/HeldLab/ProteoClade

ITIS: the Integrated Taxonomic Information System!

Jit — Fri, 30 Aug 2019 23:07:15 -0500

ITIS, the Integrated Taxonomic Information System! Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. We are a partnership of U.S., Canadian, and Mexican agencies (ITIS-North America); other organizations; and taxonomic specialists. ITIS is also a partner of Species 2000 and the Global Biodiversity Information Facility (GBIF). The ITIS and Species 2000 Catalogue of Life (CoL)partnership is proud to provide the taxonomic backbone to the Encyclopedia of Life (EOL).

https://www.itis.gov/pdf/twb_ug.pdf

Address of the bookmark: https://www.itis.gov/