Purpose in project
Showing 25 of 119 results
SoftwarereleasedJuicer is a platform for analyzing high-resolution Hi-C data.
SoftwarereleasedPython module warapping htslib C-API and samtools for accessing sam formatted alignment filesSoftware type: other
SoftwarereleasedGenerates normalized density signal from aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: file format conversion
SoftwarereleasedEvaluates a sample of paired or single-end aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: quality metric
SoftwarereleasedSignal generation for long-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
SoftwarereleasedBowtie 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 (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
SoftwarereleasedA very efficient implemenation of the the Maximal Overlap Discrete Wavelet Tranform (MODWT). See D. B. Percival and A. T. Walden (2000), Wavelet Methods for Time Series Analysis. Cambridge, England: Cambridge University Press. This is not the usual discrete wavelet transform found in, for example, gsl but an extended set of algorithms designed to overcome some problems with the usual discrete wavelet transform.
SoftwarereleasedThe snow package provides support for simple parallel computing on a network of workstations using R. A master R process calls makeCluster to start a cluster of worker processes; the master process then uses functions such as clusterCall and clusterApply to execute R code on the worker processes and collect and return the results on the master. This framework supports many forms of "embarrassingly parallel" computations.Software type: other