BOL: Related items

Circleator

Jit — Sun, 25 Jun 2017 18:04:32 -0500

The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Common uses of the tool include:

Displaying the sequence and/or genes in a GenBank flat file.
Highlighting differences and/or similarities in gene content between related organisms.
Comparing SNPs and indels between closely-related strains or serovars.
Comparing gene expression values across multiple samples or timepoints.
Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

Builds on BioPerl and the input file formats that it supports, including:
- GenBank flat files, GFF, FASTA
Accepts a number of other commonly-used datatypes and file formats:
- BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
Requires only a single configuration file whose layout mirrors that of the figure itself.
- Predefined configuration files and "track" types are supplied for common datasets.
- Advanced features allow limited analyses to be performed as a figure is drawn.
Includes an extensive set of regression tests.
Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

zPicture: A dynamic blastz alignment visualization

Archana Malhotra — Tue, 30 Jan 2018 16:03:08 -0600

zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.

Address of the bookmark: https://zpicture.dcode.org/

G-compass: a comparative genome browser

Jit — Thu, 12 Apr 2018 10:00:27 -0500

G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their ortholog information were derived from H-InvDB and its subdatabase Evola, respectively. G-compass is available for free of charge. [ Sample ]

Address of the bookmark: http://www.h-invitational.jp/g-compass/

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Jit — Fri, 24 Aug 2018 09:50:01 -0500

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

PANEV: an R package for a pathway-based network visualization

Jit — Sun, 09 Feb 2020 12:41:52 -0600

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 downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7

Address of the bookmark: https://github.com/vpalombo/PANEV

Proksee: in-depth characterization and visualization of bacterial genomes

LEGE — Tue, 09 May 2023 19:38:52 -0500

Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

Address of the bookmark: https://proksee.ca/

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Abhi — Sat, 08 Jun 2024 16:25:08 -0500

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia was inspired by Staphopia, a workflow we (Tim Read and myself) released that is targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

To highlight the use of Bactopia and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Address of the bookmark: https://bactopia.github.io/latest/

d3Network:Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.

Jit — Fri, 06 Apr 2018 12:10:45 -0500

Mike Bostock’s D3.js is great for creating interactive network graphs with JavaScript. The d3Network package makes it easy to create these network graphs from R. The main idea is that you should able to take an R data frame with information about the relationships between members of a network and create full network graphs with one command.

Address of the bookmark: http://christophergandrud.github.io/d3Network/

Interactive Market Intelligence

Pranjali Yadav — Mon, 19 Jan 2015 08:20:38 -0600

BioInformatics LLC, a premier research and advisory firm serving the life science industry, has launched groundbreaking, dynamic-data presentation platform, Interactive Market Intelligence— the only cloud-based market research analytics tool for the life science tools industry.

Superior to traditional PDF and PowerPoint reports, Interactive Market Intelligence allows end-users to filter, create and export literally thousands of views of data — all easily obtainable from a set of core metrics that include market, brand, customer and workflow analytics in well-defined segments of the life science market.

The Market for Real-Time PCR is the first in a series of topics to be explored using the Interactive Market Intelligence platform. The primary research analysis is based on a survey of 900+ international scientists performing qPCR in their laboratories.

Key data findings from "The Market for Real-Time PCR": Global market for qPCR in 2015 is estimated to be $3.6B; The average growth in qPCR throughput is expected to be at 9.8% in 2015; 22% of respondents are highly likely to switch primary suppliers of qPCR products; 50% of respondents use pre-designed primer/probe sets.

Leaflet: JavaScript libraries for interactive maps

Jit — Mon, 10 Feb 2020 01:35:07 -0600

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 tiles
- Markers
- Polygons
- Lines
- Popups
- GeoJSON
Create maps right from the R console or RStudio
Embed maps in knitr/R Markdown documents and Shiny apps
Easily render spatial objects from the sp or sf packages, or data frames with latitude/longitude columns
Use map bounds and mouse events to drive Shiny logic
Display maps in non spherical mercator projections
Augment map features using chosen plugins from leaflet plugins repository

https://rstudio.github.io/leaflet/

Address of the bookmark: https://rstudio.github.io/leaflet/