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ISMARA / Integrated System for Motif Activity Response Analysis
Enables computational reconstruction of regulatory circuitry from high-throughput data. ISMARA uses motif activity response analysis to identify the key regulators, i.e., transcription factors (TFs) and microRNAs (miRNAs) driving gene expression/chromatin state changes across the samples, the activity profiles of these regulators, their target genes, and the sites on the genome through which these regulators act. The stand-alone client application (called the ISMARA client) automates the process of pre-processing the user’s raw data on her/his own computer.
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.
A package to detect genes that show different transcript abundances between two conditions putatively caused by alterations in histone modification. Epigenomix is based on a correlation measure for integrative analysis of ChIP-seq and gene transcription data measured by RNA sequencing or microarrays. We propose quantile normalization for ChIP-seq data and a Bayesian mixture approach involving a mixture of mixtures and distributions of different type (normal and exponential) to classify transcripts based on a measure for the correlation between histone modifications and gene transcription.
A web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq allows users to contextualise their sequencing data with respect to vast amounts of public data in a few minutes without requiring any programming skills. Heat*seq currently contains over 12,000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualise user experiments. High quality figures and tables are produced and can be downloaded in multiple formats.
Allocates cells measured with single-cell RNA-seq to clones derived from low-coverage single-cell DNA-seq. clonealign is statistical method that constructs a phylogenetic tree using single-cell copy number measurements. It permits the discovery of clone-specific phenotypic properties in real cancer data. This tool is useful in the field of single cell biology including extensions for other multimodal approaches such as methylation-transcription and chromatin accessibility-transcription.
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