Detects functional signals in tag profiles from different assays such as histone ChIP-seq, TF ChiP-seq, DNase-seq and FAIRE-seq. DFilter is based on a single receiver operating characteristic – area under the curve (ROC-AUC) optimizing algorithm. This software suits for genomic signals of individual cell types diluted in cellular mixture because the proportion of marginal signals can be mistaken for noise by suboptimal algorithms.
Computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays. Phantompeakqualtools can be used to (i) Compute the predominant insert-size (fragment length) based on strand cross-correlation peak; (ii) compute data quality measures based on relative phantom peak; (iii) call peaks and regions for punctate binding datasets
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 genome-wide identification of potential chromatin– chromatin interaction (CCI) sites and loops at kilobase resolution. CISD provides two algorithms: CISD that identifies chromatin interaction sites at kilobase resolution from MNase-seq data and CISD_loop for prediction of CCIs from low-resolution HiC and data. This approach facilitates the expansion of the field of 3D genome research by allowing the exploration of more cell types, tissues and species.
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.
Visualizes next-generation sequencing (NGS) signals and sequence motif densities along genomic features using average plots and heatmaps. It can also calculate sequence motif density profiles from reference genome. SeqPlots is useful both for exploratory data analyses and preparing replicable, publication quality plots. Other features of the software include collaboration and data sharing capabilities, as well as ability to store pre-calculated result matrixes, that combine many sequencing experiments and in-silico generated tracks with multiple different features.
Produces genome-wide raw or normalized signal tracks from aligned sequencing reads. Wiggler is a program that enables production of genome-wide signal coverage tracks for ChIP-seq, DNase-seq, FAIRE-seq and MNase-seq datasets. To perform, this tool takes into account of different details: depth of sequencing, the mappabilty of the genome, different tag shifts for the different datasets being combined, or differentiates between positions.
Performs quality control for micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) data. CAM permits users to compare their data to a set of 268 historical MNase-seq datasets in human and mouse that serve as a reference. It generates nucleosome organization profiles based on promoters and custom defined regions. The tool is able to detect regions with well-positioned nucleosome arrays.
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