Showing 13 of 13 results
Software
released
Cell Ranger ATAC and Loupe Browser are software applications for analyzing and visualizing Single Cell ATAC data produced by the 10x Genomics Chromium platform.Software type: peak callerSoftware
released
Method for generating a master list / Index of DNaseI-Hypersensitive Sites ("consensus DHSs"). All code, implementation details and design by Wouter Meuleman and Eric Rynes. Docker implementation by Jemma Nelson.Software type: peak callerSoftware
released
Peak calling by GRIT for Rampage ENCODE uniform processing pipeline.Software type: peak callerSoftware
released
overlap_peaks.py is a method to select overlapping peaks among replicates and psuedo-replicatesSoftware type: peak callerSoftware
released
F-seq is a software package that generates a continuous density estimation of sequence tags mapped to a reference genome, which can be displayed using the UCSC Genome Browser. The continuous density plots are more intuitive than discrete histogram-like plSoftware type: peak callerSoftware
released
Calls hotspots and peaks on filtered alignments by hotspot2 for DNase ENCODE uniform processing pipeline.Software type: peak callerSoftware
released
GEM is a Java software package for analyzing genome wide ChIP-seq/ChIP-exo data. GEM can decompose single observed peaks into multiple binding events, determine binding event location at high spatial resolution, and discover explanatory DNA sequence motifSoftware type: peak callerSoftware
released
A ChIP-seq peak calling algorithm, implemented as an R package, that accounts for the offset in forward-strand and reverse-strand reads to improve resolution, compares enrichment in signal to background or control experiments, and can also estimate whetheSoftware type: peak caller