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Trawler
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.
FunChIP
Classifies peaks with a functional analysis of their shapes. FunChIP is an R package which consists in a series of methods for the GenomicRanges class, which sequentially add metadata columns to the GRanges, and ultimately assign each enriched region to a cluster. It assigns each peak to a cluster, defined by the functions approximating their shapes. It includes also a versatile visualization function, which automatically separates the peaks according to the clustering, and plots their shapes.
ChAsE / Chromatin Analysis and Exploration
A cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments. ChAsE is designed and developed in close collaboration with several groups of biologists and bioinformaticians with a focus on usability and interactivity. Data can be analyzed through k-means clustering, specifying presence or absence of signal in epigenetic data, and performing set operations between clusters. Results can be explored in an interactive heat map and profile plot interface and exported for downstream analysis or as high quality figures suitable for publications.
CATCHprofiles / Clustering and AlignmenT of ChIp profiles
A standalone for exhaustive pattern detection in ChIP profiling data. CATCHprofiles is built upon a computationally efficient implementation for the exhaustive alignment and hierarchical clustering of ChIP profiling data. The tool features a graphical interface for examination and browsing of the clustering results. CATCHprofiles requires no prior knowledge about functional sites, detects known binding patterns ‘‘ab initio’’, and enables the detection of new patterns from ChIP data at a high resolution, exemplified by the detection of asymmetric histone and histone modification patterns around H2A.Z-enriched sites. CATCHprofiles’ capability for exhaustive analysis combined with its ease-of-use makes it an invaluable tool for explorative research based on ChIP profiling data.
DGW / Dynamic Genome Warping
Allows clustering, alignment and clustering of epigenomic marks. DGW is based on an algorithm that enables construction of robust speech recognizers undeterred by the variability in pitch and speed of enunciation. The software can align genomic landmarks such as transcription start sites (TSSs) and first splicing sites (FSSs) on real epigenomic data from the ENCODE project. The software can be useful for exploratory data analysis of high throughput epigenomic data sets.
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