Allows analysis of ChIP-seq and other functional sequencing data. SPP is an R package providing a data processing pipeline optimized for detection of localized protein binding positions from unpaired sequence reads. This software can examine the saturation level of detected binding position to determine the amount of additional sequencing that may be necessary. It assesses also saturation properties and determines minimal saturated enrichment ratio (MSER).
Allows motif identification. cERMIT is designed to analyze current large genomic regulatory datasets such as those from ChIPchip or ChIP-seq experiments. The software makes use of the complete data without the need to pre-define or infer thresholds. It can take different data as evidence for regulatory interactions, and can optionally utilize orthologous sequences from related species to restrict the search to co-occurring motifs.
Detects motifs in large scale chromatin-immunoprecipitation (ChIP) data. Trawler is a program that can be run according two different manners: (i) a standalone version providing a pipeline that generates position weight matrices (PWMs) from the extraction and clustering of over-represented motifs; and (ii) a web application supplying the possibility to submit sequences in both FASTA or BED format, to rank predicted motifs by conservation score as well as to produce a set of background sequences.
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.
Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.
Identifies protein–DNA binding events in small bacterial and archaeal genomes. Pique facilitate downstream data visualization, curation and analysis. It also provides a suitable platform for large-scale studies of the structure and dynamic remodeling of gene-regulatory networks. This method is able to operate on systems that have genomic complexities such as IS elements, gene dosage polymorphisms and accessory genomes.
Allows to manage and analyse ChIP-seq experiments. PRI-CAT focuses on plants and particularly on Arabidopsis CHIP-seq analysis. It uses the ratio between the number of mapped reads in experimental and control data sets to returns score values per nucleotide position. The tool allows the user to fairly compare experiments thank to the ratios used are less dependent on the different number of reads sequenced in each experiment.
Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq is a multi-platform application that uses well established tools to implement pipelines for DNA-seq, CNAseq, bisulfite-seq and ChIP-seq experiments. The software incorporates a graphical user interface (GUI), designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together. The modular structure permits easy adaptation and extension.
Aims to reduce the efforts put into basic data processing for next-generation sequencing (NGS). QuickNGS enables data analysis for major applications of NGS in a batch-like operation mode. This pipeline relies on the organization of available metadata in a MySQL database which is used to control the overall workflow composed of specific software applications for different kinds of analysis.
Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.
Analyses mapped reads from diverse High-throughput sequencing (HTS) experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. Pyicos is a command line utility for the conversion and manipulation of genomic coordinates files. It facilitates HTS analysis through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Pyicos is part of the Pyicoteo suite of tools.
Assists in processing ChIP-chip and ChIP-seq data. W-ChIPeaks is a web application that employed a probe-based (or bin-based) enrichment threshold to define peaks and applied statistical methods to control false discovery rate for identified peaks. This resource includes two different web interfaces: probebased enrichment threshold level (PELT) for ChIP-chip and bin-based enrichment threshold level (BELT) for ChIP-seq.
Provides a web platform for analysis of ChIP-seq data. Nebula functionalities are: read mapping, peak calling, peak and gene annotation with genomic features and de novo motif discovery with ChIPMunk. This software also incorporates several tools for data quality control and can generate graphical output and enrichment statistics. It is designed for biologist who are inexperienced with bioinformatics.
Computes quality metrics for aligned data from ChIP-seq experiments. ChIPQC automatically calculates multiple quality metrics. This software can evaluate absolute and relative quality of individual ChIP-seq and control samples by generating a ChIP-seq experiment quality report. It can also be employed to examine samples individually without requiring the full experimental structure.
Consists of a collection of investigation approaches and displays software for microarray data. Chipster is useful for several types of high throughput data such as microarrays, proteomics and next generation sequencing (NGS). It can be employed to normalize most of the commonly used chip types and permits to utilize the remapped information. This tool is useful for RNA degradation, relative log expression (RLE), normalized unscaled standard error (NUSE) or quality control probe expression.
Provides access to a set of useful tools performing common ChIP-Seq data analysis tasks. The ChIP-Seq Web Server also includes positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The server also provides access to hundreds of publicly available data sets such as ChIP-seq data, RNA-seq data (i.e. CAGE), DNA-methylation data, sequence annotations (promoters, polyA-sites, etc.), and sequence-derived features (CpG, phastCons scores).
Enables broad and analysis of ChIP-seq data. ChIPseeqer is a comprehensive computational framework that includes: (1) gene-level annotation of peaks, (2) pathways enrichment analysis, (3) regulatory element analysis, using either a de novo approach, known or user-defined motifs, (4) nongenic peak annotation (repeats, CpG islands, duplications, published ChIP-seq datasets), (5) conservation analysis, (6) clustering analysis, (7) visualization tools, (8) integration and comparison across different ChIP-seq experiments.
An extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of next-generation sequencing (NGS) applications. Its unique features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software on local computers and computer clusters. A flexible sample annotation infrastructure efficiently handles complex sample sets and experimental designs. To simplify the analysis of widely used NGS applications, systemPipeR provides pre-configured workflows and reporting templates for RNA-seq, ChIP-seq, VAR-seq and Ribo-seq.
Performs ChIP-Seq data analysis. HiChIP allows read mapping, peak calling for punctate and diffuse binding sites and downstream functional analysis. This software offers to users several parameters to filtering out less reliability mapped reads to diminish noise to improve the quality of peak calling. It also combines methods to enhance the preprocessing and annotations of ChiP-Seq data.
Automates quality controls and data analyses on ChIP-seq and DNase-seq data. ChiLin generates comprehensive quality control reports that include comparisons with historical data derived from over 23,677 public ChIP-seq and DNase-seq samples (11,265 datasets) from eight literature-based classified categories. Therefore, ChiLin can be an attractive solution to rapidly process batches of ChIP-seq datasets in an automated manner with detailed QC reports.