ENCODE Software
All software used or developed by the ENCODE Consortium
- ENCODE Consortium116
- ENCODE Processing Pipeline50
- Alkes Price, Harvard10
- Brenton Graveley, UConn10
- Barbara Wold, Caltech8
- John Stamatoyannopoulos, UW8
- J. Michael Cherry, Stanford7
- Ali Mortazavi, UCI6
- Soumya Raychaudhuri, Harvard5
- Erez Aiden, Baylor4
- Mark Gerstein, Yale4
- Tim Reddy, Duke4
- Bill Noble, UW3
- Gene Yeo, UCSD3
- Ryan Tewhey, JAX3
- Thomas Gingeras, CSHL3
- Xinshu Grace Xiao, UCLA3
- Christina Leslie, MSKCC2
- Job Dekker, UMass2
- Michael Snyder, Stanford2
- Roderic Guigo, CRG2
- Zhiping Weng, UMass2
- Alexander Hoffmann, UCLA1
- Anshul Kundaje, Stanford1
- Chris Burge, MIT1
- ENCODE Consortium Analysis Working Group1
- Jay Shendure, UW1
- Manolis Kellis, Broad1
- Mats Ljungman, UMichigan1
- Michael Bassik, Stanford1
- Nadav Ahituv, UCSF1
- Richard Myers, HAIB1
- Robert Klein, Mount Sinai1
- Robert Waterston, UW1
- Susan Celniker, LBNL1
- Ting Wang, WUSTL1
- Yin Shen, UCSF1
Showing 25 of 272 results
- sQTLseekeR — sourcesQTLseekeR is a package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. In sQTLSeeker, splicing patterns are modeled by the relative expression of the transcripts of a gene. The most recent version of sQTLseekeR can be employed to detect genetic variant associated to any multivariate phenotypeSoftware type: variant annotation
- ggsashimi — sourcea command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments. It uses popular bioinformatics file formats, it is annotation-independent, and allows the visualization of splicing events even for large genomic regions by scaling down the genomic segments between splice sites. It is implemented in python, and internally generates R code for plotting.Software type: visualization
- Library sequencing match — sourceHouse script that was matching the guides (from an input list) to the fastq files as returned by deep sequencingSoftware type: quantification
- eFORGE — sourceeFORGE identifies tissue or cell type-specific signal by analysing a minimum set of 5 differentially methylated positions (DMPs) for overlap with DNase I hypersensitive sites (DHSs) compared to matched background DMPs and provides both graphical and tabulated outputs.Software type: integrated analysis
- GenomeStudio — sourceSoftware developed by Illumina for analysis of microarray data.Software type: other
- ptools_bin — sourceA data-sanitization software allowing raw functional genomics reads to be shared while minimizing privacy leakage, enabling principled privacy-utility trade-offs.Software type: other
- SCREEN — sourceSCREEN is a web-based visualizer for the ENCODE Registry of cCREs. Users can search for cCREs by genomic region or by associated features such as genes and SNPs, and can also visualize associated underlying annotations from the ground and integrative levels of the ENCODE Encyclopedia such as gene expression, TF ChIP-seq peaks, chromatin states, and cCRE-target gene links. Additionally, users can access ENCODE data on the functional characterization of cCREs.
- apricot — sourceapricot implements submodular optimization for the purpose of summarizing massive data sets into minimally redundant subsets that are still representative of the original data. These subsets are useful for both visualizing the modalities in the data and for training accurate machine learning models with just a fraction of the examples and compute.
- CRADLE — sourceCRADLE (Correcting Read counts and Analysis of DifferentiaLly Expressed regions) is a package that was developed to analyze STARR-seq data. CRADLE removes technical biases from sonication, PCR, mappability and G-quadruplex sturcture, and generates bigwig files with corrected read counts. CRADLE then uses those corrected read counts and detects both activated and repressed enhancers. CRADLE will help find enhancers with better accuracy and credibility.
- Croo — sourceCroo is a Python package for organizing outputs from Cromwell. Croo parses metadata.json which is an output from Cromwell and makes an organized directory with a copy (or a soft link) of each output file as described in an output definition JSON file specified by --out-def-json.Software type: framework
- Caper — sourceCaper (Cromwell Assisted Pipeline ExecutoR) is a wrapper Python package for Cromwell. Caper is based on Unix and cloud platform CLIs (curl, gsutil and aws) and provides easier way of running Cromwell server/run modes by automatically composing necessary input files for Cromwell. Also, Caper supports easy automatic file transfer between local/cloud storages (local path, s3://, gs:// and http(s)://). You can use these URIs in input JSON file or for a WDL file itself.Software type: framework
- encode_utils — sourceTools that are useful to any ENCODE Consortium submitting group, as well as the general community working with ENCODE data. Library and scripts are coded in Python.
- Check Files — sourceFiles are checked to see if the MD5 sum (both for gzipped and ungzipped) is identical to the submitted metadata, as well as run through the validateFiles program from Jim Kent's source utilities.
- liftOverThis UCSC tool converts genome coordinates and genome annotation files between assemblies.