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

 Miscellaneous 6 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 9 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 202 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 12 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 40 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 13 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 26 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, […]

GATK 3.6 – Analysis Tools for Next-generation DNA Sequencers

 DNA / Genome Analysis 1,765 views Comments Off on GATK 3.6 – Analysis Tools for Next-generation DNA Sequencers
Aug 102016
 
GATK 3.6 - Analysis Tools for Next-generation DNA Sequencers

GATK 3.6 :: 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 […]

JASPAR 2014 1.9.0 – Transcription Factor Binding Profile Database

 DNA / Genome Analysis 107 views Comments Off on JASPAR 2014 1.9.0 – Transcription Factor Binding Profile Database
Aug 102016
 
JASPAR 2014 1.9.0 - Transcription Factor Binding Profile Database

JASPAR 2014 1.9.0 :: DESCRIPTION JASPAR is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. ::DEVELOPER The Wasserman Lab :: SCREENSHOTS N/A :: REQUIREMENTS Windows/MacOsX/Linux R package/BioConductor/BioPython :: DOWNLOAD   JASPAR for BioConductor/ for R / for Biopython :: MORE INFORMATION Citation JASPAR 2014: an extensively […]

FastQ Screen 0.7.0 – Screening Application for High Througput Sequence data

 DNA / Genome Analysis 127 views Comments Off on FastQ Screen 0.7.0 – Screening Application for High Througput Sequence data
Aug 102016
 
FastQ Screen 0.7.0 - Screening Application for High Througput Sequence data

FastQ Screen 0.7.0 :: DESCRIPTION FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. :: DEVELOPER Babraham Bioinformatics :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Mac OsX/Windows Perl :: DOWNLOAD  FastQ […]