Showing 13 of 13 results

• Software

  released

  Mango — source

  Mango: a bias-correcting ChIA-PET analysis pipeline

  Software type: peak caller

• Software

  released

  edwBamFilter — source

  Remove reads from a BAM file based on a number of criteria

  Software type: filtering

• Software

  released

  trim-adapters-illumina — source

  This program will trim adapters from pair-end sequencing tags produced using the Illumina(c) platform.

  Software type: filtering

• Software

  released

  modwt — source

  A 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 discre

• Software

  released

  Spark — source

  Spark is an interactive pattern discovery and visualization approach designed with epigenomic data in mind. Spark can reveal both known and novel epigentic signatures.

  Software type: database

• Software

  released

  wigToBigWig — source

  The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. BigWig files are created initially from wiggle (wig) type files, using the program wigToBigWig. The resulting bigWig files are in an indexe

  Software type: file format conversion

• Software

  released

  ENCODE-motifs — source

  A database that uncovers the molecular basis of TF binding in the human genome based on regulatory motif analysis of all Transcription Factors (TFs) grouped by family. This allows browsing of all known motifs for each factor, curated from TRANSFAC, Jaspar

  Software type: database

• Software

  released

  atSNP — source

  An R package for screening SNPs for their potential to enhance or disrupt transcription factor binding sites. atSNP accepts as input either SNP ids or the actual coordinates of the SNPs and the alternative alleles. It uses ENCODE motifs and JASPAR motifs

• Software

  released

  RegulomeDB — source

  Identifies DNA features and regulatory elements in non-coding regions of the human genome. One can enter dbSNP IDs, BED files, VCF files, or GFF3 files. A score is returned assessing the evidence for regulatory potential. Clicking on the score reveals the

  Software type: database, variant annotation

• Software

  released

  StamPipes

  This is a focused collection of makefiles and scripts to for analysis on Illumina sample data. While this probably can't be directly used by someone not in our lab, it might be a useful reference for others.

  Software type: filtering

• Software

  released

  snow — source

  The 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

  Software type: other

• Software

  released

  bigWigToWig — source

  The binary bigWig format can be converted to the text based wig or bedGraph formats using this utility.

  Software type: file format conversion

• Software

  released

  Regulatory Elements Database — source

  Using an intuitive interface, you can 1) identify DNaseI-hypersensitive sites (DHS) within a genomic region of interest, 2) predict the target gene for DHS of interest, 3) predict the DHS that regulate a gene of interest, 4) identify clusters of similarly

  Software type: database