clusterProfiler 3.14.0 – Statistical Analysis and Visulization of Functional Profiles for Genes and Gene Clusters

clusterProfiler 3.14.0

:: DESCRIPTION

clusterProfiler implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

::DEVELOPER

Guangchuang YU,, Li-Gen Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

  clusterProfiler

:: MORE INFORMATION

Citation

OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28.
clusterProfiler: an R package for comparing biological themes among gene clusters.
Yu G1, Wang LG, Han Y, He QY.

COLOMBO 4.0 / SIGI-HMM – Statistical Analysis of Sequences of a Genome /Prediction of Genomic Islands in Prokaryotic Genomes

COLOMBO 4.0

:: DESCRIPTION

COLOMBO is a software framework equipped with a GUI for the statistical analysis of sequences of a genome. It can be equipped with different plugins that actually perform the analysis. The current version of COLOMBO is supplied with SIGI-HMM, a tool for the prediction of Genomic Islands.

::DEVELOPER

Theoretical Computer Science and Algorithmic Methods , at the University of Göttingen.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java
  • Perl

:: DOWNLOAD

COLOMBO

:: MORE INFORMATION

Citation

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R.
BMC Bioinformatics. 2006 Mar 16;7:142.

RNApasta 1.6 – RNA Structural Alignment & Statistical Analysis

RNApasta 1.6

:: DESCRIPTION

RNApasta is a utility for collecting statistics from aligned and structurally annotated RNA sequences.RNApasta is a java utility intended to work with RNA structural alignments, including the motifs of stem-loops and pseudoknots.  RNApasta can perform a variety of statistical analyses, and has editing capabilities intended to be useful with alignments that contain variable data such as the presence or absence of stem-loops or pseudoknots across sequences.  RNApasta can read Rfam-stockholm formatted files or pasta formatted files.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNApasta

:: MORE INFORMATION

Citation

Malmberg, R., Shaw, T., and Cai, L. (2010)
RNApasta: a tool for analysis of RNA structural alignments,
Int J Bioinform Res Appl. 2010;6(6):571-83.

PLABSTAT 20110711 – Statistical Analysis of Plant Breeding Experiments

PLABSTAT 20110711

:: DESCRIPTION

PLABSTAT (PLAnt Breeding STATistical program) is a concise package to analyse plant breeding experiments (lattices, unreplicated and multi-factor experiments)..PLABSTAT estimates basic statistics, e.g. variance, skewness, curtosis, and coefficients of correlation. Simple or multiple linear regression including path coefficients are also calculated.

::DEVELOPER

H. Friedrich Utz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • windows

:: DOWNLOAD

 PLABSTAT

:: MORE INFORMATION

mlegp 3.1.4 – Statistical Analysis for Computer Models of Biological Systems

mlegp 3.1.4

:: DESCRIPTION

 mlegp (Maximum Likelihood Estimates of Gaussian Processes) is an R package to analyze computer models of complex systems.

::DEVELOPER

Bioinformatics Laboratory at Eastern Connecticut State University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows / MacOsX
  • R Package

:: DOWNLOAD

 mlegp

:: MORE INFORMATION

Citation

Dancik GM, Dorman KS (2007)
mlegp: statistical analysis for computer models of biological systems using R.
Bioinformatics (2008) 24 (17): 1966-1967.

metagenomeSeq 1.12.1 – Statistical Analysis of Sparse High-throughput Sequencing data

metagenomeSeq 1.12.1

:: DESCRIPTION

metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

::DEVELOPER

HCBravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

  metagenomeSeq

:: MORE INFORMATION

Citation:

Nat Methods. 2013 Dec;10(12):1200-2. doi: 10.1038/nmeth.2658. Epub 2013 Sep 29.
Differential abundance analysis for microbial marker-gene surveys.
Paulson JN1, Stine OC, Bravo HC, Pop M.

Jstacs 2.2 – Java Framework for Statistical Analysis and Classification of Biological Sequences

Jstacs 2.2

:: DESCRIPTION

Jstacs is an open source Java library, which focuses on the statistical analysis of biological sequences instead. Jstacs comprises an efficient representation of sequence data and provides implementations of many statistical models with generative and discriminative approaches for parameter learning. Using Jstacs, classifiers can be assessed and compared on test datasets or by cross-validation experiments evaluating several performance measures.

::DEVELOPER

Jstacs Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 Jstacs

:: MORE INFORMATION

Citation

Michael Seifert, Marc Strickert, Alexander Schliep and Ivo Grosse
Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models
Bioinformatics (2011) 27 (12): 1645-1652.

CFAssay 1.4.0 – Statistical analysis for the Colony Formation Assay

CFAssay 1.4.0

:: DESCRIPTION

CFAssay provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.

::DEVELOPER

Herbert Braselmann <braselm at helmholtz-muenchen.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • R/ Bioconductor

:: DOWNLOAD

 CFAssay

:: MORE INFORMATION

Citation

CFAssay: statistical analysis of the colony formation assay.
Braselmann H, Michna A, Heß J, Unger K.
Radiat Oncol. 2015 Nov 4;10(1):223. doi: 10.1186/s13014-015-0529-y.

TCGA2STAT 1.2 – Simple TCGA Data Access for Integrated Statistical Analysis in R

TCGA2STAT 1.2

:: DESCRIPTION

TCGA2STAT automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.

:: DEVELOPER

Liu Lab, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • R

:: DOWNLOAD

 TCGA2STAT

:: MORE INFORMATION

Citation

TCGA2STAT: Simple TCGA Data Access for Integrated Statistical Analysis in R.
Wan YW, Allen GI, Liu Z.
Bioinformatics. 2015 Nov 14. pii: btv677.

RNAither 2.18.0 – Statistical analysis of high-throughput RNAi screens

RNAither 2.18.0

:: DESCRIPTION

RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes.

::DEVELOPER

Lars Kaderali <lars.kaderali at tu-dresden.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 RNAither

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 1;25(5):678-9. doi: 10.1093/bioinformatics/btp014. Epub 2009 Jan 25.
RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens.
Rieber N1, Knapp B, Eils R, Kaderali L.