├── CHANGELOG.md ├── DESCRIPTION ├── NAMESPACE ├── R └── data.R ├── README.md ├── data-raw ├── ITFP │ ├── 01-download-html.sh │ ├── 02-tables.sh │ ├── 03-download-tables.sh │ ├── 04-html-to-text.sh │ ├── 05-text-to-tsv.sh │ ├── README.md │ └── regulated_genes.tsv.gz ├── Marbach2016 │ ├── FANTOM5_individual_networks │ │ ├── 394_individual_networks │ │ │ └── synoviocyte.txt.bz2 │ │ └── _README.txt │ └── download.sh ├── Neph2012 │ ├── README.md │ ├── human_2013-09-16 │ │ ├── AG10803-DS12374 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── AoAF-DS13513 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── CD20-DS18208 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── CD34-DS12274 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── GM06990-DS7748 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── GM12865-DS12436 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HAEpiC-DS12663 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HAh-DS15192 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HCF-DS12501 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HCM-DS12599 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HCPEpiC-DS12447 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HEEpiC-DS12763 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HFF-DS15115 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HIPEpiC-DS12684 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HMF-DS13368 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HMVEC_LLy-DS13185 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HMVEC_dBlAd-DS13337 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HMVEC_dBlNeo-DS13242 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HMVEC_dLyNeo-DS13150 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HPAF-DS13411 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HPF-DS13390 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HPdLF-DS13573 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HRCE-DS10666 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HSMM-DS14426 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HVMF-DS13981 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── HepG2-DS7764 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── IMR90-DS13219 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── K562-DS9767 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── NB4-DS12543 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── NHA-DS12800 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── NHDF_Ad-DS12863 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── NHDF_Neo-DS11923 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── NHLF-DS12829 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── SAEC-DS10518 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── SKNSH-DS8482 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── SkMC-DS11949 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── all.filtered.transfac │ │ ├── fBrain-DS11872 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── fHeart-DS12531 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── fLung-DS14724 │ │ │ └── genes.regulate.genes.bz2 │ │ ├── gene2entrez.tsv │ │ ├── hESCT0-DS11909 │ │ │ └── genes.regulate.genes.bz2 │ │ └── hTH1-DS7840 │ │ │ └── genes.regulate.genes.bz2 │ └── mm9_2013-12-03 │ │ ├── MEL-DS13036 │ │ └── genes.regulate.genes.bz2 │ │ ├── ZhBTc4-DS15236 │ │ └── genes.regulate.genes.bz2 │ │ ├── ZhBTc4-DS17562 │ │ └── genes.regulate.genes.bz2 │ │ ├── ZhBTc4-DS17616 │ │ └── genes.regulate.genes.bz2 │ │ ├── m3134-DS8497 │ │ └── genes.regulate.genes.bz2 │ │ ├── m416B-DS14099 │ │ └── genes.regulate.genes.bz2 │ │ ├── mA20-DS16695 │ │ └── genes.regulate.genes.bz2 │ │ ├── mATn-DS17070 │ │ └── genes.regulate.genes.bz2 │ │ ├── mATr-DS20149 │ │ └── genes.regulate.genes.bz2 │ │ ├── mB-DS16168 │ │ └── genes.regulate.genes.bz2 │ │ ├── mB-DS17866 │ │ └── genes.regulate.genes.bz2 │ │ ├── mBrain-DS12727 │ │ └── genes.regulate.genes.bz2 │ │ ├── mCJ7-DS13320 │ │ └── genes.regulate.genes.bz2 │ │ ├── mGenitalFatPad-DS18182 │ │ └── genes.regulate.genes.bz2 │ │ ├── mHeart-DS18138 │ │ └── genes.regulate.genes.bz2 │ │ ├── mKidney-DS13948 │ │ └── genes.regulate.genes.bz2 │ │ ├── mLiver-DS14605 │ │ └── genes.regulate.genes.bz2 │ │ ├── mLung-DS14479 │ │ └── genes.regulate.genes.bz2 │ │ ├── mNIH_3T3-DS16900 │ │ └── genes.regulate.genes.bz2 │ │ ├── mRetina-DS20004 │ │ └── genes.regulate.genes.bz2 │ │ ├── mTN-DS16171 │ │ └── genes.regulate.genes.bz2 │ │ ├── mTN-DS17080 │ │ └── genes.regulate.genes.bz2 │ │ ├── mTR-DS17864 │ │ └── genes.regulate.genes.bz2 │ │ ├── mThymus-DS18819 │ │ └── genes.regulate.genes.bz2 │ │ └── mfBrain-DS14536 │ │ └── genes.regulate.genes.bz2 ├── TRED │ ├── 01-download-factors.py │ ├── 02-download-targets.py │ ├── 03-gid-to-entrez.py │ ├── README.md │ ├── factors.tsv.gz │ ├── gid_entrez.tsv.gz │ └── targets.tsv.gz ├── TRRUST │ ├── README.md │ ├── download.sh │ └── trrust_rawdata.txt.gz ├── UCSC │ ├── README.md │ ├── knownGene.txt.gz │ └── knownToLocusLink.txt.gz └── make_rdata.R ├── data └── tftargets.rda ├── figures ├── ENCODE_histogram.png ├── ITFP_histogram.png ├── Marbach2016_histogram.png ├── Marbach2016_targets_vs_weight.png ├── Marbach2016_weights_histogram.png ├── Neph2012_1_histogram.png ├── TRED_histogram.png ├── TRRUST_histogram.png └── transcription_factor_image.jpg └── man ├── ENCODE.Rd ├── ITFP.Rd ├── Marbach2016.Rd 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