Showing 11 of 11 results
Software
released
Measures consistency between replicates in high-throughput experiments. Also uses reproducibility in score rankings between peaks in each replicate to determine an optimal cutoff for significance. The core IDR R package can be downloaded from the IDR doSoftware type: quality metric, filteringSoftware
released
BWA is a software package for mapping low-divergent sequences based on a Burrows-Wheeler index against a large reference genome, such as the human genome. Publications for the short read alignment component is found at PMID: 19451168, while PMID: 2008050Software type: alignerSoftware
released
Used to generate three quality metrics: NSC, RSC, and PBC. The NSC (Normalized strand cross-correlation) and RSC (relative strand cross-correlation) metrics use cross-correlation of stranded read density profiles to measure enrichment independently of peSoftware type: quality metric, filteringSoftware
released
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (eSoftware
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
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetics: that is, set theory on the genome. For example, bedtools allows one to intersect, mergeSoftware type: file format conversionSoftware
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