FamAgg 0.99.9 – Pedigree Analysis and Familial Aggregation

FamAgg 0.99.9

:: DESCRIPTION

FamAgg is an open source R package that contains both established and novel methods to investigate familial aggregation of traits in large pedigrees.

::DEVELOPER

Johannes Rainer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R / BioConductor

:: DOWNLOAD

 FamAgg

:: MORE INFORMATION

Citation

FamAgg: an R Package to Evaluate Familial Aggregation of Traits in Large Pedigrees.
Rainer J, Taliun D, D’Elia Y, Pattaro C, Domingues FS, Weichenberger CX.
Bioinformatics. 2016 Jan 22. pii: btw019.

MuCor – Mutation Aggregation and Correlation

MuCor

:: DESCRIPTION

MuCor is software to aggregate variant information sourced from multiple VCF files (and some others, see below) into a variety of summary files with varying levels of detail and statistics.

::DEVELOPER

blachly lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

  MuCor

:: MORE INFORMATION

Citation:

MuCor: Mutation Aggregation and Correlation.
Kroll KW, Eisfeld AK, Lozanski G, Bloomfield CD, Byrd JC, Blachly JS.
Bioinformatics. 2016 Jan 23. pii: btw028

MASCP Gator 1.1 – Proteomics Aggregation Utility

MASCP Gator 1.1

:: DESCRIPTION

MASCP Gator is a proteomics aggregation utility  that queries and aggregates information from a variety of online Arabidopsis proteomic resources.

::DEVELOPER

The Joint BioEnergy Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MASCP gator: an overview of the Arabidopsis proteomic aggregation portal.
Mann GW, Calley PC, Joshi HJ, Heazlewood JL.
Front Plant Sci. 2013 Oct 23;4:411. doi: 10.3389/fpls.2013.00411

HyDRA – Hybrid Distance-Score Rank Aggregation software for Gene Prioritization

HyDRA

:: DESCRIPTION

HyDRA is a new approach to genomic data aggregation which combines the advantages of score-based and combinatorial aggregation techniques.

::DEVELOPER

Minji Kim

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

 HyDRA

:: MORE INFORMATION

Citation

HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation.
Kim M, Farnoud F, Milenkovic O.
Bioinformatics. 2014 Nov 18. pii: btu766.

PASTA 2.0 – Protein Aggregation Prediction

PASTA 2.0

:: DESCRIPTION

PASTA (Prediction of amyloid structure aggregation) is a web server for the analysis of amino acid sequences. It predicts which portions of a given input sequence are more likely to stabilize the cross-beta core of fibrillar aggregates.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASTA

:: MORE INFORMATION

Citation:

PASTA 2.0: an improved server for protein aggregation prediction.
Walsh I, Seno F, Tosatto SC, Trovato A.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W301-7. doi: 10.1093/nar/gku399.

Antonio Trovato, Flavio Seno and Silvio C.E. Tosatto.
The PASTA server for protein aggregation prediction
Protein Engineering Design & Selection, 20(10):521-523. (2007)

AGGRESCAN – Prediction and Evaluation of “hot spots” of Aggregation in Polypeptides

AGGRESCAN

:: DESCRIPTION

AGGRESCAN is a web-based software for the prediction of aggregation-prone segments in protein sequences, the analysis of the effect of mutations on protein aggregation propensities and the comparison of the aggregation properties of different proteins or protein sets.

::DEVELOPER

Xavier Daura

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Feb 27;8:65.
AGGRESCAN: a server for the prediction and evaluation of “hot spots” of aggregation in polypeptides.
Conchillo-Solé O1, de Groot NS, Avilés FX, Vendrell J, Daura X, Ventura S.

CAGT r132 – Clustering AGgregation Tool

CAGT r132

:: DESCRIPTION

CAGT is a tool to analyze the heterogeneity and diversity of the magnitude, shape and orientation of patterns of functional genomics signal tracks (such as histone modification ChIP-seq signal) around a specific set of defined genomic anchor points (e.g. TF binding sites or TSSs)

::DEVELOPER

The Batzoglou Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • Matlab

:: DOWNLOAD

 CAGT

:: MORE INFORMATION

Citation

Genome Res. 2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111.
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.
Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A.

ACT – Aggregation and Correlation Toolbox for analyses of Genome Tracks

ACT

:: DESCRIPTION

The ACT (aggregation and correlation toolbox) is an aggregation and correlation toolbox for analyses of genome tracks.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  ACT

:: MORE INFORMATION

Citation

J Jee*, J Rozowsky*, KY Yip*, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein.
ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. (2011)
Bioinformatics. 2011 Apr 15;27(8):1152-4.