Integrates workflow technology and in-built access to bioinformatics resources including remote data warehouses and tools. Galaxy permits users without programming skills to conduct computational analysis through the Web. It builds a succession of tools to perform multistep studies and is able to conserve the complete provenance of each analysis step. This platform offers drag and drop functionalities to ease the construction of workflows.
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Performs peak finding and downstream data analysis for next-generation sequencing analysis. HOMER affords several tools and methods to make use of ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and other types of functional genomics sequencing data sets. This software offers support to UCSC visualization, peaks annotation, quantification of transcripts and repeats or differential features, enrichment and expression.
Analyzes data generated by short read sequencers. MACS is a standalone software dedicated to the forecasting of protein-DNA interaction sites from ChIP-Seq. The application is able to: (i) model the distance d and shifting tags by d/2 to enable the spatial resolution of the predicted sites; (ii) capture local biases in the genome by exploiting a dynamic λ local parameter and (iii) evaluate the false discovery rate (FDR) for each detected peak.
A web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery.
A system to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.
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Discover our proposed protocols.
They are easy to use or edit to meet your needs.
They are easy to use or edit to meet your needs.
LSD1 promotes oxidative metabolism of white adipose tissue
Tools (3):
Bowtie, IGV, HOMER
Topics (13):
CAGE analysis, scRNA-seq analysis, DNase-seq analysis, Ribo-seq analysis, WGS analysis, WES analysis, De novo sequencing analysis, RNA-seq analysis, ChIP-seq analysis, sRNA-seq analysis, Metatranscriptomic sequencing analysis, Metagenomic sequencing analysis, CLIP-seq analysis
Nitrogen stress response and stringent response are coupled in Escherichia coli
Tools (3):
Bowtie, IGV, SISSRs
Topics (18):
CAGE analysis, scRNA-seq analysis, DNase-seq analysis, Ribo-seq analysis, WGS analysis, WES analysis, De novo sequencing analysis, RNA-seq analysis, ChIP-seq analysis, sRNA-seq analysis, Metatranscriptomic sequencing analysis, Metagenomic sequencing analysis, CLIP-seq analysis, Escherichia coli, Ribonucleotides, Heterocyclic Compounds, 2-Ring, Purine Nucleotides, Nitrogen
EED orchestration of heart maturation through interaction with HDACs is H3K27me3 independent
Tools (3):
BWA, MACS, IGV
Topics (4):
De novo sequencing analysis, ChIP-seq analysis, DNase-seq analysis, Mus musculus
Separase prevents genomic instability by controlling replication fork speed
Tools (5):
BCL2FASTQ Conversion Software, FastQC, MACS, CEAS, SRA
Topics (3):
ChIP-seq analysis, DNase-seq analysis, Homo sapiens
Dot1 regulates nucleosome dynamics by its inherent histone chaperone activity in yeast
Tools (5):
Bowtie2, MACS, deepTools, BEDTools, bwtool
Topics (8):
De novo sequencing analysis, ChIP-seq analysis, DNase-seq analysis, Homo sapiens, Saccharomyces cerevisiae, Ribonucleotides, Heterocyclic Compounds, 2-Ring, Purine Nucleotides