R-SAP 1.1 – RNA-Seq Analysis pipeline

R-SAP 1.1

:: DESCRIPTION

 R-SAP is a user-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. R-SAP accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values.

::DEVELOPER

McDonald Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

 R-SAP

:: MORE INFORMATION

Citation:

Mittal VK, McDonald JF. 2012.
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data.
Nucleic Acid Reseaech. Jan. 28;

MEGA 11 – Molecular Evolutionary Genetics Analysis

MEGA 11

:: DESCRIPTION

MEGA (Molecular Evolutionary Genetics Analysis)is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

::DEVELOPER

MEGA Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

MEGA

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Dec;30(12):2725-9. doi: 10.1093/molbev/mst197. Epub 2013 Oct 16.
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011)
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Molecular Biology and Evolution (2011)doi: 10.1093/molbev/msr121 First published online: May 4, 2011

AltAnalyze 2.1.4.3 – Microarry and RNA-Seq Analysis

AltAnalyze 2.1.4.3

:: DESCRIPTION

AltAnalyze is an easy-to-use application for microarry and RNA-Seq analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for conventional arrays (RMA summarization, QC, statistics, annotation, clustering, lineage characterization and gene-set enrichement).

::DEVELOPER

the Nathan Salomonis laboratory at Cincinnati Children’s Hosptial Medical Center and the University of Cincinnati.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Python

:: DOWNLOAD

 AltAnalyze

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W755-62. Epub 2010 May 31.
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M.

ISAMBARD v2.3.1 – Intelligent System for Analysis, Model Building And Rational Design of Biomolecules

ISAMBARD v2.3.1

:: DESCRIPTION

ISAMBARD is a Python-based framework for structural analysis and rational design of biomolecules, with a particular focus on parametric modelling of proteins.

::DEVELOPER

Woolfson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ISAMBARD

:: MORE INFORMATION

Citation

Wood CW, Heal JW, Thomson AR, Bartlett GJ, Ibarra AÁ, Brady RL, Sessions RB, Woolfson DN.
ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.
Bioinformatics. 2017 Oct 1;33(19):3043-3050. doi: 10.1093/bioinformatics/btx352. PMID: 28582565; PMCID: PMC5870769.

CLUMPHAP 1.1 – Haplotype-based Association Analysis

CLUMPHAP 1.1

:: DESCRIPTION

CLUMPHAP implements a novel method for association testing based on clustering similar haplotypes (Knight et al. Submitted). This represents an extension of the basic methodology used in CLUMP, a program designed for the analysis of multi-allelic markers (Sham and Curtis 1995). CLUMPHAP calculates chi-squared statistics for binary partitions of haplotypes, where the number of partitions is reduced by allowing only those that are supported by a hierarchical cluster analysis of the haplotypes. CLUMPHAP obtains the empirical significance level of the largest chi-square statistic by a permutation procedure in which multiple permuted datasets (where the case-control labels have been randomly re-assigned) are subjected to exactly the same procedure of haplotype partitioning and calculation of largest chi-square statistic. Incidentally, this permutation procedure accounts for not only the inflation of the test statistic due to the maximization over the multiple ways of partitioning the haplotypes, but also for the uncertainty in haplotype phase of the individual subjects (Curtis and Sham 2006). The results are easy to interpret, a significant result suggests that a disease causing variant is present on haplotypes in the group which has an increased overall frequency in cases. CLUMPHAP reports the cluster pattern that resulted in the highest chi-squared along with the corresponding statistic and the empirical p-value.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CLUMPHAP

:: MORE INFORMATION

Citation:

Knight J, Curtis D, Sham PC (submitted)
CLUMPHAP: A simple tool for performing haplotype-based association analysis.
Genet Epidemiol. 2008 Sep;32(6):539-45.

MetaboliteDetector 3.3 – Deconvolution and Analysis of GC/MS Data

MetaboliteDetector 3.3

:: DESCRIPTION

Metabolite Detector is a QT4 based software package for the analysis of GC-MS based metabolomics data. The software is especially intended for the analysis of high resoluted GC-MS chromatograms which accumulate during high throughput based metabolmics experiments.

::DEVELOPER

MetaboliteDetector Team

:: SCREENSHOTS

MetaboliteDetector

:: REQUIREMENTS

  • Linux/ Windows 

:: DOWNLOAD

 MetaboliteDetector

:: MORE INFORMATION

Citation

Anal Chem. 2009 May 1;81(9):3429-39. doi: 10.1021/ac802689c.
MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis.
Hiller K, Hangebrauk J, J?ger C, Spura J, Schreiber K, Schomburg D.

dmGWAS 3.0 – Genome-wide Association Studies (GWAS) Analysis

dmGWAS 3.0

:: DESCRIPTION

dmGWAS is designed to identify significant protein-protein interaction (PPI) modules and, from which, the candidate genes for complex diseases by an integrative analysis of GWAS dataset(s) and PPI network.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 dmGWAS

:: MORE INFORMATION

Citation:

EW_dmGWAS: Edge-weighted dense module search for genome-wide association studies and gene expression profiles.
Wang Q, Yu H, Zhao Z, Jia P.
Bioinformatics. 2015 Mar 24. pii: btv150.

Jia P, Zheng S, Long J, Zheng W, and Zhao Z (2011)
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.
Bioinformatics 27(1):95-102

LinRegPCR 20210614 – Analysis of Quantitative PCR Data

LinRegPCR 20210614

:: DESCRIPTION

LinRegPCR is a program for the analysis of quantitative RT-PCR (qPCR) data resulting from monitoring the PCR reaction with SYBR green or similar fluorescent dyes. The program determines a baseline fluorescence and does a baseline subtraction. Then a Window-of-Linearity is set and PCR efficiencies per sample are calculated. With the mean PCR efficiency per amplicon, the Ct value per sample and the fluorescence threshold set to determnine the Ct, the starting concentration per sample, expressed in arbitrary fluorescence units, is calculated

::DEVELOPER

J. M. Ruijter, S. van der Velden,A. Ilgun @ Heart Failure Research Center (HFRC)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Excel

:: DOWNLOAD

 LinRegPCR

:: MORE INFORMATION

Citation

Ramakers C, Ruijter JM, Deprez RH, Moorman AF. (2003)
Assumption-free analysis of quantitative real-time PCR data
Neurosci Lett 2003 Mar 13;339(1): 62-66

SWAPSC 1.0 – Sliding Windows Analysis Procedure to detect Selective Constraints in Protein-coding Genes

SWAPSC 1.0

:: DESCRIPTION

SWAPSC is the software of the Sliding Window Analysis Procedure to detect Selective Constraints in protein-coding genes. The program estimates rates of nucleotide substitutions at specific codon regions in each branch of a phylogenetic tree. The program uses several sets of simulated sequence alignments to estimate the probability of synonymous and non-synonymous nucleotide substitutions. Thereafter, a statistical analysis is conducted to determine the optimum window size to detect selective constraints. Finally, the optimum window size is slid along the real alignment and a test for significance of the estimated number of synonymous and non-synonymous nucleotide substitutions in each sliding step is conducted.

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 SWAPSC

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Nov 1;20(16):2867-8. Epub 2004 May 6.
SWAPSC: sliding window analysis procedure to detect selective constraints.
Fares MA.

CAPS 2.0 – Coevolution Analysis using Protein Sequences

CAPS 2.0

:: DESCRIPTION

CAPS (Coevolution Analysis using Protein Sequences) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites.

CAPS Online Version

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 CAPS

:: MORE INFORMATION

Citation

CAPS: coevolution analysis using protein sequences.
Fares MA, McNally D.
Bioinformatics. 2006 Nov 15;22(22):2821-2. Epub 2006 Sep 27.