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.
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.
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.
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.
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.
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.
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.
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.
A set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system; most (18/20) were also implemented as standalone, fully functional R scripts. The set consists of four full turnkey pipelines and 16 component modules. The turnkey pipelines in Kepler allow data provenance tracking. Implementation emphasized use of common R packages and widely-used external tools (e.g., MACS for peak finding), along with custom programming. ChIPSeqWorkflows presents comprehensive solutions and easily repurposed code blocks for ChIP-seq analysis and pipeline creation. Tasks include mapping raw reads, peakfinding via MACS, summary statistics, peak location statistics, summary plots centered on the transcription start site (TSS), gene ontology, pathway analysis, and de novo motif finding, among others.
Allows analysis and visualization of interval-based genomic data. GeMSE implements a set of abstractions for data analysis, exploration and visualization. The software supports primitives for data explorations spanning from select, sort, and discretize clustering, and pattern extraction. It enables interactive analytics (IA), an approach suggested for evaluating processing results and for designing and adapting next-generation sequencing (NGS) data analysis pipelines.
Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease footprint sequencing (MNase-seq), DNase hypersensitivity sequencing (DNase-seq), and transposase-accessible chromatin using sequencing ATAC-seq datasets. CIPHER provides an analysis mode that accomplishes complex bioinformatics tasks such as enhancer prediction. It supplies functions to integrate various NGS datasets together.
Provides a ChIP-Seq data analysis pipeline that performs all the essential steps in one script. Workflow_of_CHIPSeq aims to help biologists with few bioinformatics skills in their analysis of ChIP-Seq data. It encompasses all necessary steps of ChIP-Seq data analyses, including trimming, mapping and Quality Control (QC), peak calling, peak annotation, and visualization. This tool starts by aligning fastq files to a reference genome.
Permits ChIP-seq data investigation. Crunch starts from raw read quality control, through read mapping, peak detection and annotation, and includes comprehensive DNA sequence motif analysis. It is based on Bayesian and Gaussian mixture models. This tool can model the observed ChIP-seq signal in terms of novel and known regulatory motifs by combining de novo motif finding with binding site prediction for a large collection of known regulatory motifs.
Automates processing of a collection of ChIPSeq or ATAC-Seq data starting from the gzip compressed fastq files. ChIPSeqFPro is a pipeline that performs the quality control using FastQC, mapping to the human genome or mouse using BWA mapper. It then converts sam to bam using samtools view, creates statistics on bam files using samtools flagstat, peak calling with MACS. It creates high resolution bigwig files from bam files using a custom script bam2bigwig that invokes bedtools bamtobed and UCSC scripts, bedItemOverlapCount, bedGraphToBigWig and fetchChromSizes.
Decrypts key biological features from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data. ChIPdig aims to assist experimentalists process multi-sample ChIP-seq data. It can map reads to a reference genome, normalize and compare ChIP-seq data sets corresponding to different targets or conditions, display coverage in a set of regions thanks to heatmaps and a comparative metaplot.
Provides an assortment of approaches for ChIP-seq datasets analysis. echipp supplies various methods and functions for alignment, quality control and statistical. The application is a pipeline composed of a package coupled to multiple scripts and is able to handle various datasets including the large ones.
Assists users in analyzing and interpreting datasets. Rosalind is a genomics analysis platform that aims to simplify the practice of genomic data interpretation. It enables users to exploit the potential of genomic information, from DNA sequencing to microarrays and mass spectrometers, while reducing costs. The user can drag-and-drop files, identify kits and follow the NCBI bio-sample data model.
Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq, MeDIP-seq and ChIP-seq experiments. This tool includes standard differential expression analysis for different experimental conditions, as well as differential splicing analysis. It can notice variants in the transcriptome and gene fusion events.
A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
Helps to process short read data for chipseq experiments. chiseq provides a function that plots one or two coverage vectors over a relatively small interval in the genome. It can identify and produce summary statistics for differentially expressed peaks. The tool allows the user to estimate summaries of the distribution of fragment lengths in a shortread experiment.
A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB, and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides, and a user interface designed to enable both novice and experienced users of RNA-Seq data.
Spans all steps of ChIP-seq data analysis. CASSys is a program that supplies functionalities ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome and the detection of enriched regions to various follow-up analyses. Moreover, to perform, this tool employs a selection of software tools for read mapping and peak detection.