RNAmap2D 1.7.5 – Visualization of 2D maps of RNA Structures

RNAmap2D 1.7.5

:: DESCRIPTION

RNAMAP2D is a software to the analysis of contact maps of RNA structures and protein – RNA complexes. The program deals with modified base pairs which are very frequent in RNA and includes ligands and ions which plays key roles in forming and stabilizing RNA structures. What is more, it is possible to show on the computed map whether some of the identified contacts are recognized as belonging to one of the 12 base pairs families, are canonical Watson – Crick pairs, or are 4 classes of stacking interactions. The overlap of the 2D maps of two structures can be easily calculated, providing a measure of RNA structure similarity.

::DEVELOPER

Bujnicki Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

  RNAmap2D

:: MORE INFORMATION

TDFragMapper 1.0 – Visualization tool for Evaluating Experimental parameters in top-down Proteomics

TDFragMapper 1.0

:: DESCRIPTION

TDFragMapper can deal with multiple fragmentation methods and can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics.

::DEVELOPER

MSBIO – INSTITUT PASTEUR

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • The .NET framework

:: DOWNLOAD

TDFragMapper

:: MORE INFORMATION

Citation

Dhenin J, Lima DB, Dupré M, Chamot-Rooke J.
TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics.
Bioinformatics. 2021 Nov 18:btab784. doi: 10.1093/bioinformatics/btab784. Epub ahead of print. PMID: 34792554.

ProteinVR 1.0.7 – Browser-based, virtual-reality visualization of Molecular Structures

ProteinVR 1.0.7

:: DESCRIPTION

ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

ProteinVR

:: MORE INFORMATION

 

V-Phaser 2.0 / V-Profiler 1.0 – Variant Calling and Visualization tools to Identify Biological Mutations in Diverse populations

V-Phaser 2.0 / V-Profiler 1.0

:: DESCRIPTION

V-Phaser is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. V-Phaser combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity.

V-Profiler takes a read alignment and a list of accepted variants at each location in the alignment (such as would be generated by V-Phaser) and analyzes the intra-host diversity of a genome. This can be done at the nucleotide level over the whole sequence, at the codon level for each gene specified in a list, and at the haplotype level for any region delimited (note that the region must not exceed a read length, and is preferably of shorter length such as an epitope or a loop of interest).

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 V-Phaser  / V-Profiler

:: MORE INFORMATION

Citation

BMC Genomics. 2013 Oct 3;14:674. doi: 10.1186/1471-2164-14-674.
V-Phaser 2: variant inference for viral populations.
Yang X, Charlebois P, Macalalad A, Henn MR, Zody MC.

PLoS Comput Biol. 2012;8(3):e1002417. doi: 10.1371/journal.pcbi.1002417. Epub 2012 Mar 15.
Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.
Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, Henn MR.

CRISPRO v1.0.2 – Analysis and Visualization of Saturating Mutagenesis CRISPR Screens

CRISPRO v1.0.2

:: DESCRIPTION

CRISPRO is a pipeline to process next generation sequnecing data from saturating mutagenesis CRISPR screens, whereby sgRNAs are mapped to amino acids of the protein, allowing for the inference of functional scores for amino acids in a protein.

::DEVELOPER

bauer lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  Windows
  • Python
  • R

:: DOWNLOAD

CRISPRO

:: MORE INFORMATION

Citation

Schoonenberg VAC, Cole MA, Yao Q, Macias-Treviño C, Sher F, Schupp PG, Canver MC, Maeda T, Pinello L, Bauer DE.
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis.
Genome Biol. 2018 Oct 19;19(1):169. doi: 10.1186/s13059-018-1563-5. PMID: 30340514; PMCID: PMC6195731.

AVAtar 0.4.11 – Analysis and Visualization of Alteration data

AVAtar 0.4.11

:: DESCRIPTION

Avatar features interactively customizable alteration plots, extensive data import capabilities and a multi-objective optimization algorithm to find alteration patterns, e.g. gene sets with mutually exclusive alterations or small gene sets with high sample coverage.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

AVAtar

:: MORE INFORMATION

Citation

Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffman TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA.
Analysis, identification and visualization of subgroups in genomics.
Brief Bioinform. 2021 May 20;22(3):bbaa217. doi: 10.1093/bib/bbaa217. Erratum in: Brief Bioinform. 2021 Jul 06;: PMID: 32954413; PMCID: PMC8138884.

IdeogramBrowser 0.20.4 – Visualization of Genomic Aberrations using Affymetrix SNP Arrays

IdeogramBrowser 0.20.4

:: DESCRIPTION

IdeogramBrowser  was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

IdeogramBrowser

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Java
:: DOWNLOAD

 IdeogramBrowser

:: MORE INFORMATION

Citation

André Müller, Karlheinz Holzmann and Hans A. Kestler
Visualization of genomic aberrations using Affymetrix SNP arrays
Bioinformatics (2007) 23 (4): 496-497.

Haplosuite 1.1 – R package for Haplotype Clustering and Visualization

Haplosuite 1.1

:: DESCRIPTION

Haplosuite is a collection of R codes, including HAPLOSIM and HAPVISUAL, for the purpose of clustering haplotypes and haplotype visualization

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 Haplosuite

:: MORE INFORMATION

Citation

Teo YY and Small KS. (2010)
A novel method for haplotype clustering and visualization.
Genetic Epidemiology, 34(1), 34-41

spatialTIME 1.2.0 / iTIME – Visualization and Analysis of Immunofluorescence data

spatialTIME 1.2.0 / iTIME

:: DESCRIPTION

spatialTIME (Spatial Analysis of Vectra Immunoflourescent Data) is to perform basic analysis and plotting of IF data from Vectra.

iTIME (interactive Tumor Immune MicroEnvironment) is a shiny application that creates interactive figures for examining spatial organization of individual tumors and provide basic spatial and summary information.

::DEVELOPER

Fridley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

spatialTIME  / iTIME

:: MORE INFORMATION

Citation:

Creed JH, Wilson CM, Soupir AC, Colin-Leitzinger CM, Kimmel GJ, Ospina OE, Chakiryan NH, Markowitz J, Peres LC, Coghill A, Fridley BL.
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data.
Bioinformatics. 2021 Nov 4:btab757. doi: 10.1093/bioinformatics/btab757. Epub ahead of print. PMID: 34734969.

Helium 190903 – Helium Pedigree Visualization Framework

Helium 190903

:: DESCRIPTION

Helium is a generic platform in which various data types can be shown in a pedigree context and we hope to have a beta version available soon that users can download and experiment with.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

 Helium

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Helium

 :: MORE INFORMATION