ArticleBMC genomics2016
The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Ribosome stalling is a signal for metabolic regulation by the ribotoxic stress response.Cell metabolism · 2022Article
- Productive visualization of high-throughput sequencing data using the SeqCode open portable platform.Scientific reports · 2021Article
- Computational identification and experimental characterization of preferred downstream positions in human core promoters.PLoS computational biology · 2021Article
- AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.Scientific reports · 2021Article
- Conserved DNA sequence features underlie pervasive RNA polymerase pausing.Nucleic acids research · 2021Article
- Transcriptional Profiling of STAT1 Gain-of-Function Reveals Common and Mutation-Specific Fingerprints.Frontiers in immunology · 2021Article
- Plasma Membrane Calcium ATPase Regulates Stoichiometry of CD4Frontiers in immunology · 2021Article
- Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue.Cellular and molecular life sciences : CMLS · 2021Article
- Readthrough of stop codons under limiting ABCE1 concentration involves frameshifting and inhibits nonsense-mediated mRNA decay.Nucleic acids research · 2020Article
- EPD in 2020: enhanced data visualization and extension to ncRNA promoters.Nucleic acids research · 2020Article
- CSA: a web service for the complete process of ChIP-Seq analysis.BMC bioinformatics · 2019Article
- PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix.Bioinformatics (Oxford, England) · 2018Article
- TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets.BMC genomics · 2018Article
- MGA repository: a curated data resource for ChIP-seq and other genome annotated data.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data.
resultsHere we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade.
conclusionsThe various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.