ccPDB 2.0 – Compilation and Creation of datasets from PDB

ccPDB 2.0

:: DESCRIPTION

ccPDB is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links.

::DEVELOPER

ccPDB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank.
Agrawal P, Patiyal S, Kumar R, Kumar V, Singh H, Raghav PK, Raghava GPS.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/bay142.

ccPDB: compilation and creation of data sets from Protein Data Bank.
Singh H, Chauhan JS, Gromiha MM; Open Source Drug Discovery Consortium, Raghava GP.
Nucleic Acids Res. 2012 Jan;40(Database issue):D486-9. doi: 10.1093/nar/gkr1150.

NIS-Elements Viewer 4.11.0 – View Image files and Datasets

NIS-Elements Viewer 4.11.0

:: DESCRIPTION

NIS-Elements Viewer is a free standalone program to view image files and datasets. It offers the same powerful view and image selection modes as the NIS-Elements core packages: Volume View with 3D Rendering, Tile View for Time, Z and Multipoint datasets, and Slice View for Z and Time datasets. The NIS-Elements Viewer also has the same look and feel as the NIS-Elements core packages. For example, calibrations, and binary layers (thresholded objects) created in the core package also port over to the NIS-Elements Viewer. In addition, image header information and experimental information such as time interval, Z step and device parameters are accessible (Windows version only). Saving ND datasets to TIFF files is also built into the NIS-Elements Viewer.

::DEVELOPER

Nikon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOSX

:: DOWNLOAD

NIS-Elements Viewer

:: MORE INFORMATION

Frida 1.1.0 – FRamework for Image Dataset Analysis

Frida 1.1.0

:: DESCRIPTION

Frida (FRamework for Image Dataset Analysis) is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility. Frida is open source and written in 100% Java. Frida makes use of functionality from the NIH’s ImageJ application.

::DEVELOPER

JHU Tissue MicroArray Core Facility

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

Frida

:: MORE INFORMATION

Citation:

Cornish T, Morgan J, Gurel B, and De Marzo AM.
FrIDA: An open source framework for image dataset analysis.
Arch. Pathol. Lab. Med. 132:856 (2008). Originally presented at Advancing Practice, Instruction and Innovation Through Informatics: Pittsburgh, PA, 2007.

Myrna 1.2.3 – Cloud-scale Differential Gene Expression for RNA-seq

Myrna 1.2.3

:: DESCRIPTION

Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.

::DEVELOPER

Ben Langmead, Kasper Hansen, and Jeffrey Leek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bowtie

:: DOWNLOAD

  Myrna

:: MORE INFORMATION

Citation

Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11.
Cloud-scale RNA-sequencing differential expression analysis with Myrna.
Langmead B, Hansen KD, Leek JT.

DiffSplice 0.1.2beta – Discover Alternative Splicing Variants present in an RNA-seq dataset

DiffSplice 0.1.2beta

:: DESCRIPTION

DiffSplice is a novel tool for discovering and quantitating alternative splicing variants present in an RNA-seq dataset, without relying on annotated transcriptome or pre-determined splice pattern. For two groups of samples, DiffSplice further utilizes a non-parametric permutation test to identify significant differences in expression at both gene level and transcription level. DiffSplice takes as input the SAM files that supply the alignment of the RNA-seq reads on the reference genome, obtained from an RNA-seq aligner like MapSplice. The results of DiffSplice are summarized as a decomposition of the genome and can be visualized using the UCSC genome browser.

::DEVELOPER

Bioinformatics Lab @CS.UKy.edu

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 DiffSplice

:: MORE INFORMATION

Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15.
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J.

GOModeler – Hypothesis Testing of Functional Genomics Datasets

GOModeler

:: DESCRIPTION

GOModeler allows users to conduct a hypothesis driven interrogation of their functional genomics datasets

:: DEVELOPER

AgBase, Department of Basic Science,College of Veterinary Medicine, Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S29. doi: 10.1186/1471-2105-11-S6-S29.
GOModeler–a tool for hypothesis-testing of functional genomics datasets.
Manda P, Freeman MG, Bridges SM, Jankun-Kelly TJ, Nanduri B, McCarthy FM, Burgess SC.

Chimerascan 0.4.5a – Detect Gene Fusions in Paired-end RNA Sequencing (RNA-Seq) Datasets

Chimerascan 0.4.5a

:: DESCRIPTION

Chimerascan is a  software for detecting gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.

::DEVELOPER

The Michigan Center for Translational Pathology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Chimerascan

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Oct 15;27(20):2903-4. Epub 2011 Aug 11.
ChimeraScan: a tool for identifying chimeric transcription in sequencing data.
Iyer MK, Chinnaiyan AM, Maher CA.

DatasetAssess – Estimate Error Rates in High-throughput Protein Interaction datasets

DatasetAssess

:: DESCRIPTION

 DatasetAssess is a tool to estimate error rates in high-throughput protein interaction datasets and other functional genomic data.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 DatasetAssess

:: MORE INFORMATION

Citation:

Gilchrist, M.A., Salter, L.A., Wagner, A. (2004)
A statistical framework for combining and interpreting proteomic datasets.
Bioinformatics 20, 689-700

BroadPeak – Broad Peak calling algorithm for Diffuse ChIP-seq Datasets

BroadPeak

:: DESCRIPTION

BroadPeak is an algorithm for the identification of broad peaks from diffuse ChIP-seq datasets.

::DEVELOPER

Jordan Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • R Program

:: DOWNLOAD

 BroadPeak 

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):492-3. doi: 10.1093/bioinformatics/bts722. Epub 2013 Jan 7.
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Wang J, Lunyak VV, Jordan IK.

HAPGEN 2.2.0 – Simulate Case Control Datasets at SNP Markers

HAPGEN 2.2.0

:: DESCRIPTION

HAPGEN simulates case control datasets at SNP markers. The new version can now simulate multiple disease SNPs on a single chromosome, on the assumption that each disease SNP acts independently and are in Hardy-Weinberg equilibrium. We also supply a R package that can simulate interaction between the disease SNPs.

::DEVELOPER

Zhan SuJonathan Marchini , Peter Donnelly

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX /  Linux

:: DOWNLOAD

 HAPGEN

:: MORE INFORMATION

Citation

Chris C. A. Spencer, Zhan Su, Peter Donnelly, Jonathan Marchini (2009)
Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip.
PLoS Genet 5(5).