Allows data-mining and visualization of next-generation sequencing (NGS) samples such as enrichment patterns of DNA-interacting proteins at functional genomic regions. ngs.plot has a built-in database of functional elements that facilitates the management of genomic coordinates for users. This software supports large sequencing data and is available through the Galaxy tool shed.
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Allows the integrative analysis of ChIP-chip/seq data across platforms and between laboratories. MM-ChIP proceeds by modeling the characteristic fragment size of the sequenced ChIP-DNA library for each individual data source. It uses then the 3’ direction to represent the protein-DNA interaction sites. Finally, a sliding window is used to score the significance of signal enrichment in the ChIP samples by measuring and comparing tags within the same windows between ChIP.
Facilitates several typical operations related to the quantification of the sequencing signal in a set of genomic regions. compEpiTools provides a number of methods to score these data in regions of interest, leading to the identification of enhancers, lncRNAs, and RNAPII stalling/elongation dynamics. It allows a fast and comprehensive annotation of the resulting genomic regions, and the association of the corresponding genes with non-redundant GeneOntology terms.
A general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab can improve performance of binding site predictions by allowing users to integrate several motif discovery tools (including AlignAce, BioProspector, ChIPMunk, MEME, MotifSampler, Priority and Weeder) as well as different types of data, for instance phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, TF-TF interactions, TF-expression and target gene expression.
Performs the analysis of sequencing data from cross-linking, ligation and sequencing of hybrids (CLASH) experiments. hyb is able to recognize chimeric reads in other applications as well as for the analysis of UV cross-linking and analysis of cDNAs (CRAC), crosslinking and immunoprecipitation (CLIP), and RNA-Seq data. This tool can be useful and applicable to any next-generation sequencing datasets.
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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.
Niche WNT5A regulates the actin cytoskeleton during regeneration of hematopoietic stem cells
Tools (4):
HTSFilter, DESeq2, TopGO, ISMARA
Topics (5):
Transcription analysis, CAGE analysis, sRNA-seq analysis, RNA-seq analysis, Metatranscriptomic sequencing analysis
Nuclear PKC θ facilitates rapid transcriptional responses in human memory CD4+ T cells through p65 and H2B phosphorylation
Tools (3):
CEAS, HOMER, ISMARA
Topics (1):
ChIP-seq analysis
Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data
Tools (3):
DREM, T-profiler, ISMARA
Topics (4):
Transcription analysis, CAGE analysis, sRNA-seq analysis, RNA-seq analysis