ENCODE DCC

Pinned Repositories

atac-seq-pipeline
ENCODE ATAC-seq pipeline
Language:Python388 25 314174
checkfiles
Files 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 jksrc.
Language:Python2 17 00
chip-seq-pipeline
ENCODE Uniform processing pipeline for ChIP-seq
Language:Python120 39 253
chip-seq-pipeline2
ENCODE ChIP-seq pipeline
Language:Python246 25 176123
encoded
Metadata database for ENCODE project
Language:JavaScript110 30 3351
kentUtils
UCSC command line bioinformatic utilities
Language:C168 45 095
pyencoded-tools
Language:Jupyter Notebook10 32 213
rna-seq-pipeline
Language:Python141 17 4262
snovault
The SnoVault general purpose hybrid object-relational database
Language:Python16 32 228
WranglerScripts
Collection of scripts used by the wranglers to interact with the servers
Language:Python5 25 04

ENCODE DCC's Repositories

ENCODE-DCC/atac-seq-pipeline
ENCODE ATAC-seq pipeline
Language:Python388 25 314174
ENCODE-DCC/chip-seq-pipeline2
ENCODE ChIP-seq pipeline
Language:Python246 25 176123
ENCODE-DCC/kentUtils
UCSC command line bioinformatic utilities
Language:C168 45 095
ENCODE-DCC/rna-seq-pipeline
Language:Python141 17 4262
ENCODE-DCC/encoded
Metadata database for ENCODE project
Language:JavaScript110 30 3351
ENCODE-DCC/hic-pipeline
HiC uniform processing pipeline
Language:WDL57 11 2324
ENCODE-DCC/caper
Cromwell/WDL wrapper for Python
Language:Python55 11 8818
ENCODE-DCC/long-read-rna-pipeline
ENCODE long read RNA-seq pipeline
Language:wdl44 10 313
ENCODE-DCC/wgbs-pipeline
ENCODE whole-genome bisulfite sequencing (WGBS) pipeline
Language:Python29 12 1114
ENCODE-DCC/snovault
The SnoVault general purpose hybrid object-relational database
Language:Python16 32 228
ENCODE-DCC/pyencoded-tools
Language:Jupyter Notebook10 32 213
ENCODE-DCC/dnase-seq-pipeline
ENCODE DNase-seq pipeline
Language:WDL6 11 14
ENCODE-DCC/encValData
Language:AngelScript5 24 06
ENCODE-DCC/valis-hpgv
High performance WebGL genome visualization
Language:TypeScript5 3 21
ENCODE-DCC/genomic-data-service
Flask based web service providing genomic region search, based on regulomedb.org
Language:Python4 14 12
ENCODE-DCC/accession
Python module to upload experiment files and metadata to the ENCODE Portal
Language:Python3 11 3
ENCODE-DCC/geo-submission
Language:Python3 22 02
ENCODE-DCC/checkfiles
Files 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 jksrc.
Language:Python2 17 00
ENCODE-DCC/imputation_challenge
ENCODE Imputation Challenge scoring & validation scripts
Language:Python2 13 1
ENCODE-DCC/segway-pipeline
Language:Python2 11 01
ENCODE-DCC/snovault-search
Language:Python2 11 00
ENCODE-DCC/d3-sequence-logo
Sequence Logo generation in d3.js
Language:JavaScript1 9 0
ENCODE-DCC/regulome-encoded
Temp repo for regulome development
Language:JavaScript1 17 24
ENCODE-DCC/autouri
Recursive localization for various types of URIs
Language:Python9 11
ENCODE-DCC/coalesce_s3_log_glue_spark
Glue pyspark job to combine s3 access logs to parquet
Language:Python7 0
ENCODE-DCC/correlation_robustness
Language:Python8 02
ENCODE-DCC/filemetadata_dynamoDB
Load selected encode file metadata to dynamoDB
Language:Python7 0
ENCODE-DCC/google-sheet-metadata-submitter
ENCODE metadata submitter based on Google Sheet and Apps script
Language:JavaScript7 0
ENCODE-DCC/ihec-processing
IHEC processing
Language:WDL7 0
ENCODE-DCC/kentUtils_bin_v381
kentUtils_bin_v381 (binary from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)
Language:Shell10 0