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

 Genetics & Pedigree 469 views Comments Off on T-BAPS 1.0 – T-RFLP Bayesian Analysis of Population Structures
Jul 032018
 
T-BAPS 1.0 - T-RFLP Bayesian Analysis of Population Structures

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 […]

TreeMap 3.0b – Compare Host & Parasite Trees

 Phylogenetic Analysis 1,514 views Comments Off on TreeMap 3.0b – Compare Host & Parasite Trees
Jan 142018
 
TreeMap 3.0b - Compare Host & Parasite Trees

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 . […]

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

 DNA / Genome Analysis 2,906 views Comments Off on GATK 3.8-0 – Analysis Tools for Next-generation DNA Sequencers
Aug 102017
 
GATK 3.8-0 - Analysis Tools for Next-generation DNA Sequencers

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 […]

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

 Miscellaneous 213 views Comments Off on PathScore – A Web tool for Identifying Altered Pathways in Cancer data
Aug 102016
 
PathScore - A Web tool for Identifying Altered Pathways in Cancer data

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 […]

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

 RNA Analysis 234 views Comments Off on RNAcommender v0.1-beta.1 – Genome-wide Recommendation of RNA-protein Interaction
Aug 102016
 
RNAcommender v0.1-beta.1 - Genome-wide Recommendation of RNA-protein Interaction

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 […]

mlegp 3.1.4 – Statistical Analysis for Computer Models of Biological Systems

 System Biology & Modeling 379 views Comments Off on mlegp 3.1.4 – Statistical Analysis for Computer Models of Biological Systems
Aug 102016
 
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 […]

shinyGEO – Identifying Biomarkers in Gene Expression Omnibus datasets

 Genetics & Pedigree 280 views Comments Off on shinyGEO – Identifying Biomarkers in Gene Expression Omnibus datasets
Aug 102016
 
shinyGEO - Identifying Biomarkers in  Gene Expression Omnibus datasets

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 […]

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

 Genetics & Pedigree 409 views Comments Off on HaploShare 1.02 – Find Shared Haplotypes among Patients from a common recent Ancestor
Aug 102016
 
HaploShare 1.02 - Find Shared Haplotypes among Patients from a common recent Ancestor

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 87 views Comments Off on SRinversion – Detection of Short Inversions in Human Genome using Next Generation Sequencing Data
Aug 102016
 
SRinversion - Detection of Short Inversions in Human Genome using Next Generation Sequencing Data

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 […]

PRODIGY – Predicting the Binding Affinity of Protein-protein Complexes

 3D molecular model 257 views Comments Off on PRODIGY – Predicting the Binding Affinity of Protein-protein Complexes
Aug 102016
 
PRODIGY - Predicting the Binding Affinity of Protein-protein Complexes

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, […]