admin

T-BAPS 1.0 – T-RFLP Bayesian Analysis of Population Structures

 Genetics & Pedigree 442 views Comments Off on T-BAPS 1.0 – T-RFLP Bayesian Analysis of Population Structures
Jul 032018
 

T-BAPS 1.0

:: DESCRIPTION

T-BAPS (T-RFLP Bayesian Analysis of Population Structures) is a free Windows package for performing clustering analysis using T-RFLP data. T-RFLP is a newly developed molecular fingerprinting technique mainly used to investigate population structures in microbial communities. Details of the method can be found in: Tang, J., Tao J., Urakawa, H. and Corander, J. T-BAPS: a Bayesian statistical tool for comparison of microbial communities using terminal-restriction fragment length polymorphism (T-RFLP) data.

::DEVELOPER

Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 T-BAPS

:: MORE INFORMATION

Citation:

Stat Appl Genet Mol Biol. 2007;6:Article30. Epub 2007 Nov 6.
T-BAPS: a Bayesian statistical tool for comparison of microbial communities using terminal-restriction fragment length polymorphism (T-RFLP) data.
Tang J, Tao J, Urakawa H, Corander J.

TreeMap 3.0b – Compare Host & Parasite Trees

 Phylogenetic Analysis 1,411 views Comments Off on TreeMap 3.0b – Compare Host & Parasite Trees
Jan 142018
 

TreeMap 3.0b

:: DESCRIPTION

TreeMap is an experimental program for comparing host and parasite trees. TREEMAP performs cophylogeny mapping from a dependent evolutionary tree (e.g., a group of parasites) into an independent one (e.g., the hosts of those parasites), in order to recover the best possible coevolutionary explanation for the relationship between the two . The archetypal example is of the coevolution of pocket gophers and their chewing lice.

::DEVELOPER

Dr. Michael Charleston

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

TreeMap

:: MORE INFORMATION

Citation

M. A. Charleston and D. L. Robertson.
Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny.
Syst Biol, 51(3):528-535, Jun 2002.

GATK 3.8-0 – Analysis Tools for Next-generation DNA Sequencers

 DNA / Genome Analysis 2,739 views Comments Off on GATK 3.8-0 – Analysis Tools for Next-generation DNA Sequencers
Aug 102017
 

GATK 3.8-0

:: DESCRIPTION

GATK (The Genome Analysis Toolkit) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of efficiently accessing the next-generation sequencing data, researchers and developers are free to focus on their specific analysis algorithms. This not only vastly improves the productivity of developers, who can quickly write new analyses, but also results in tools that are efficient and robust, and can benefit from improvements to a common data management engine.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GATK

:: MORE INFORMATION

Citation

Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Nature Genetics 43, 491–498 (2011) doi:10.1038/ng.806

PathScore – A Web tool for Identifying Altered Pathways in Cancer data

 Miscellaneous 181 views Comments Off on PathScore – A Web tool for Identifying Altered Pathways in Cancer data
Aug 102016
 

PathScore

:: DESCRIPTION

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients.

::DEVELOPER

Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • MySQL

:: DOWNLOAD

 PathScore

:: MORE INFORMATION

Citation

PathScore: a web tool for identifying altered pathways in cancer data.
Gaffney SG, Townsend JP.
Bioinformatics. 2016 Aug 8. pii: btw512.

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

 RNA Analysis 208 views Comments Off on RNAcommender v0.1-beta.1 – Genome-wide Recommendation of RNA-protein Interaction
Aug 102016
 

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.

mlegp 3.1.4 – Statistical Analysis for Computer Models of Biological Systems

 System Biology & Modeling 363 views Comments Off on mlegp 3.1.4 – Statistical Analysis for Computer Models of Biological Systems
Aug 102016
 

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.

shinyGEO – Identifying Biomarkers in Gene Expression Omnibus datasets

 Genetics & Pedigree 196 views Comments Off on shinyGEO – Identifying Biomarkers in Gene Expression Omnibus datasets
Aug 102016
 

shinyGEO

:: DESCRIPTION

shinyGEO is a web-based application for performing differential expression and survival analysis on Gene Expression Omnibus datasets

::DEVELOPER

Bioinformatics Laboratory at Eastern Connecticut State University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 shinyGEO

:: MORE INFORMATION

Citation

shinyGEO: a web-based application for analyzing Gene Expression Omnibus datasets.
Dumas J, Gargano MA, Dancik GM.
Bioinformatics. 2016 Aug 8. pii: btw519.

HaploShare 1.02 – Find Shared Haplotypes among Patients from a common recent Ancestor

 Genetics & Pedigree 349 views Comments Off on HaploShare 1.02 – Find Shared Haplotypes among Patients from a common recent Ancestor
Aug 102016
 

HaploShare 1.02

:: DESCRIPTION

HaploShare was designed to find shared haplotypes among patients from a common recent ancestor.

::DEVELOPER

Paed Lab @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HaploShare

:: MORE INFORMATION

SRinversion – Detection of Short Inversions in Human Genome using Next Generation Sequencing Data

 DNA / Genome Analysis 74 views Comments Off on SRinversion – Detection of Short Inversions in Human Genome using Next Generation Sequencing Data
Aug 102016
 

SRinversion

:: DESCRIPTION

SRinversion is a framework to analyze poorly mapped or unmapped reads by splitting and re-aligning them for the purpose of inversion detection.

::DEVELOPER

Paed Lab @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • Perl

:: DOWNLOAD

 SRinversion

:: MORE INFORMATION

Citation

SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads.
Chen R, Lau YL, Zhang Y, Yang W.
Bioinformatics. 2016 Aug 8. pii: btw516

PRODIGY – Predicting the Binding Affinity of Protein-protein Complexes

 3D molecular model 229 views Comments Off on PRODIGY – Predicting the Binding Affinity of Protein-protein Complexes
Aug 102016
 

PRODIGY

:: DESCRIPTION

PRODIGY (PROtein binDIng enerGY prediction) webserver predict of the binding affinity in protein-protein complexes.

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 PRODIGY

:: MORE INFORMATION

Citation

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A.
Bioinformatics. 2016 Aug 8. pii: btw514.