RECLU 1.0 – Clustering pipeline with multiple scales for Capped Analysis of Gene Expression (CAGE) datasets

 Cluster Analysis 29 views Comments Off on RECLU 1.0 – Clustering pipeline with multiple scales for Capped Analysis of Gene Expression (CAGE) datasets
Feb 082016
 

RECLU 1.0

:: DESCRIPTION

RECLU is a reproducible clustering pipeline with multiple scales using capped analysis of gene expression (CAGE). This program discoveries numerous alternative transcription start sites (TSSs) with the biological implication for your sample.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 RECLU

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Apr 25;15(1):269. doi: 10.1186/1471-2164-15-269.
RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).
Ohmiya H, Vitezic M, Frith MC, Itoh M, Carninci P, Forrest AR, Hayashizaki Y, Lassmann T1; FANTOM Consortium.

clusterMaker2 0.9.5 – Creat and Visualize Cytoscape Clusters

 Cluster Analysis 377 views Comments Off on clusterMaker2 0.9.5 – Creat and Visualize Cytoscape Clusters
Feb 082016
 
clusterMaker2 0.9.5 - Creat and Visualize Cytoscape Clusters

clusterMaker2 0.9.5 :: DESCRIPTION UCSF clusterMaker is a Cytoscape plugin that unifies different clustering techniques and displays into a single interface. Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and k-means for clustering expression or genetic data; and MCL, transitivity clustering, affinity propagation, MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity […]

GenePattern 3.9.6 – Genomic Analysis Platform

 Bioinformatics Platform 812 views Comments Off on GenePattern 3.9.6 – Genomic Analysis Platform
Feb 082016
 
GenePattern 3.9.6 - Genomic Analysis Platform

GenePattern 3.9.6 :: DESCRIPTION GenePattern is a powerful genomic analysis platform that provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. GenePattern […]

PyroTrimmer 1.1 – Preprocessor of Metagenome Sequences

 DNA / Genome Analysis 0 views Comments Off on PyroTrimmer 1.1 – Preprocessor of Metagenome Sequences
Feb 072016
 
PyroTrimmer 1.1 - Preprocessor of Metagenome Sequences

PyroTrimmer 1.1 :: DESCRIPTION PyroTrimmer is a program that trims barcodes, linkers, primers, and sequence region with low quality scores from 454 sequence reads. ::DEVELOPER PyroTrimmer team :: SCREENSHOTS :: REQUIREMENTS Windows/Linux Java :: DOWNLOAD  PyroTrimmer :: MORE INFORMATION Citation J Microbiol. 2012 Oct;50(5):766-9. doi: 10.1007/s12275-012-2494-6. PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences. […]

InfMod3DGen – Inferential Modeling of 3D Chromatin Structure

 3D molecular model 1 views Comments Off on InfMod3DGen – Inferential Modeling of 3D Chromatin Structure
Feb 072016
 
InfMod3DGen - Inferential Modeling of 3D Chromatin Structure

InfMod3DGen :: DESCRIPTION InfMod3DGen is a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. ::DEVELOPER InfMod3DGen team :: SCREENSHOTS N/A :: REQUIREMENTS Windows/Linux MatLab :: DOWNLOAD  InfMod3DGen :: MORE INFORMATION Citation Nucleic Acids Res. 2015 Apr 30;43(8):e54. doi: 10.1093/nar/gkv100. Inferential modeling of 3D chromatin structure. Wang S, Xu J, […]

MetaNet – Network Construction and Biologically Significant Module Detection

 System Biology & Modeling 0 views Comments Off on MetaNet – Network Construction and Biologically Significant Module Detection
Feb 072016
 
MetaNet - Network Construction and Biologically Significant Module Detection

MetaNet :: DESCRIPTION MetaNet is a software tool in MATLAB for network construction and biologically significant module detection. ::DEVELOPER MetaNet team :: SCREENSHOTS N/A :: REQUIREMENTS Windows/Linux MatLab :: DOWNLOAD  MetaNet :: MORE INFORMATION Citation Network construction and structure detection with metagenomic count data. Liu Z, Lin S, Piantadosi S. BioData Min. 2015 Dec 12;8:40. […]

iSuc-PseOpt – Identifying lysine Succinylation Sites in proteins

 Protein Sequence Analysis 0 views Comments Off on iSuc-PseOpt – Identifying lysine Succinylation Sites in proteins
Feb 072016
 
iSuc-PseOpt - Identifying lysine Succinylation Sites in proteins

iSuc-PseOpt :: DESCRIPTION The web-server iSuc-Opt used to predict the lysine succinylation in protein. ::DEVELOPER JCI BioInfo Lab :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD   NO :: MORE INFORMATION Citation iSuc-PseOpt: Identifying lysine succinylation sites in proteins by incorporating sequence-coupling effects into pseudo components and optimizing imbalanced training dataset. Jia J, Liu […]

pRNAm-PC – Predicting N6-methyladenosine sites in RNA sequences

 RNA Analysis 1 views Comments Off on pRNAm-PC – Predicting N6-methyladenosine sites in RNA sequences
Feb 072016
 
pRNAm-PC - Predicting N6-methyladenosine sites in RNA sequences

pRNAm-PC :: DESCRIPTION The web-server pRNAm-PC is used to predict the dentify the N6-methyladenosine (m6A). ::DEVELOPER JCI BioInfo Lab :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD   NO :: MORE INFORMATION Citation pRNAm-PC: Predicting N6-methyladenosine sites in RNA sequences via physical-chemical properties. Liu Z, Xiao X, Yu DJ, Jia J, Qiu WR, Chou […]

iPPBS-Opt – Identifying Protein-Protein Binding Sites

 Protein Sequence Analysis 0 views Comments Off on iPPBS-Opt – Identifying Protein-Protein Binding Sites
Feb 072016
 
iPPBS-Opt - Identifying Protein-Protein Binding Sites

iPPBS-Opt :: DESCRIPTION The web-server iPPBS-Opt used to predict the Protein-Protein Binding Sites(PPBS). ::DEVELOPER JCI BioInfo Lab :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD   NO :: MORE INFORMATION Citation iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets. Jia J, Liu Z, Xiao X, Liu B, […]

pSuc-Lys – Predict Lysine Succinylation sites in Proteins with PseAAC and Ensemble Random Forest Approach

 Protein Sequence Analysis 0 views Comments Off on pSuc-Lys – Predict Lysine Succinylation sites in Proteins with PseAAC and Ensemble Random Forest Approach
Feb 072016
 
pSuc-Lys - Predict Lysine Succinylation sites in Proteins with PseAAC and Ensemble Random Forest Approach

pSuc-Lys :: DESCRIPTION The web-server pSuc-Lys used to predict the lysine succinylation in protein. ::DEVELOPER JCI BioInfo Lab :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD   NO :: MORE INFORMATION Citation pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach. Jia J, Liu Z, Xiao X, Liu B, […]