Nucleosee – Visual Genome-wide search of Nucleosome Patterns

Nucleosee

:: DESCRIPTION

Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Nucleosee

:: MORE INFORMATION

Citation

Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019).
Genome-wide search of nucleosome patterns using visual analytics.
Bioinformatics, 35(13), 2185-2192

KimTree 2.0.1 – Inferring Population Histories using Genome-wide Allele Frequency data

KimTree 2.0.1

:: DESCRIPTION

KimTree is a program aimed at estimating divergence times on a diffusion time scale from large single nucleotide polymorphism (SNP) data

::DEVELOPER

KimTree team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KimTree

:: MORE INFORMATION

Citation

Gautier M and Vitalis R (2013)
Inferring population histories using genome-wide allele frequency data.
Molecular Biology and Evolution 30: 654-668

MAGeCK 0.5.9.2 / MAGeCK-VISPR – Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout + Visualization of CRISPR Screens

MAGeCK 0.5.9.2 / MAGeCK-VISPR

:: DESCRIPTION

MAGeCK is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.

MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 MAGeCK ,MAGeCK-VISPR

:: MORE INFORMATION

Citation

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.
Li W, Köster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS.
Genome Biol. 2015 Dec 16;16:281. doi: 10.1186/s13059-015-0843-6.

Genome Biol. 2014;15(12):554.
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS.

SNPAAMapperT2K – Genome-wide SNP Downstream Analysis and Annotation Pipeline

SNPAAMapperT2K

:: DESCRIPTION

SNPAAMapperT2K is a genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI .tbl data files (e.g. Arabidopsis).

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PErl

:: DOWNLOAD

 SNPAAMapperT2K

:: MORE INFORMATION

Citation

Bioinformation. 2014 Nov 27;10(11):711-5. doi: 10.6026/97320630010711. eCollection 2014.
SNPAAMapperT2K: A genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI.tbl data files.
Bai Y

IGG 3.0 – Integrate Genotypes for genome-wide Genetic studies

IGG 3.0

:: DESCRIPTION

IGG (Integrate Genotypes for genome-wide Genetic studies) is an open-source Java package with graphic interface to efficiently and consistently integrate genotypes across high throughput genotyping platforms (e.g., Affymetrix and Illumina), the HapMap genotype repository (http://www.hapmap.org/), and even genotypes from the collaborators’ projects. It is equipped with a series of functions to control qualities of genotype integration and to flexibly export genotypes for genetic studies as well.

::DEVELOPER

Miao-xin Li ,The University of Hong Kong

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 IGG

:: MORE INFORMATION

Citation

Li et al. (2009)
IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis.
Bioinformatics 25(11):1449-50.

RNAcommender v0.1-beta.1 – Genome-wide Recommendation of RNA-protein Interaction

RNAcommender v0.1-beta.1

:: DESCRIPTION

RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure.

::DEVELOPER

Gianluca Corrado

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 RNAcommender 

:: MORE INFORMATION

Citation

RNAcommender: genome-wide recommendation of RNA-protein interactions.
Corrado G, Tebaldi T, Costa F, Frasconi P, Passerini A.
Bioinformatics. 2016 Aug 8. pii: btw517.

NPLB 1.0.0 – Learn de novo Promoter Architectures from Genome-wide TSSs

NPLB 1.0.0

:: DESCRIPTION

NPLB is an efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide TSSs, without relying on known promoter elements.

::DEVELOPER

NPLB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 NPLB

:: MORE INFORMATION

Citation

No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites.
Mitra S, Narlikar L.
Bioinformatics. 2015 Nov 2. pii: btv645.

FounderTracker – Genome-wide Detection of Founder Mutations in Cancer using Dense Tumor SNP Profiles

FounderTracker

:: DESCRIPTION

FounderTracker is a computational method for detecting significantly recurrent identity by descent (IBD) in a set of haplotypes. This tool was designed for the discovery of founder mutations in dense SNP array data from a population sample of tumors.

::DEVELOPER

Cartes d’Identite des Tumeurs (CIT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FounderTracker

:: MORE INFORMATION

Citation

PLoS One. 2012;7(5):e35897. doi: 10.1371/journal.pone.0035897. Epub 2012 May 2.
Identity by descent mapping of founder mutations in cancer using high-resolution tumor SNP data.
Letouzé E, Sow A, Petel F, Rosati R, Figueiredo BC, Burnichon N, Gimenez-Roqueplo AP, Lalli E, de Reyniès A.

GWIPS-viz – Genome Wide Information on Protein Synthesis

GWIPS-viz

:: DESCRIPTION

GWIPS-viz aims to provide on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique

::DEVELOPER

GWIPS-viz team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteomics. 2015 Mar 3. doi: 10.1002/pmic.201400603.
GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms.
Michel AM1, Ahern AM, Donohue CA, Baranov PV.

HiTSelect 20140708 – High-throughput Genome Wide Screen Deconvolution Software

HiTSelect 20140708

:: DESCRIPTION

HiTSelect is a software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. HiTSelect provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.

::DEVELOPER

Diaz Lab , Jun S. Song’s Research Group

:: SCREENSHOTS

HiTSelect

:: REQUIREMENTS

  • Windows /Linux/ MacOsX

:: DOWNLOAD

 HiTSelect

:: MORE INFORMATION

Citation

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.
Diaz AA, Qin H, Ramalho-Santos M, Song JS.
Nucleic Acids Res. 2014 Nov 26. pii: gku1197.