Add initial scrap

Just did the samples and datasets, there's an example of a programatic
query once we indentify some that we want

all_samples.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:9777fcdb104250dbb3577905f481a99f2f8bec7103b3d6af907e3878079d61d8
+size 49728

datasets.csv

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+,Paper identifier,Protocols,Organisms,Published?,Median QC score,ATAC-seq,RNA-seq,ChIP-seq,3D seq,Other seq
+1,Aeby2020decapping,PRO-seq,M. musculus,Yes,1.0,No,Yes,No,No,No
+2,Agarwal2021kdm1a,"other, GRO-seq",M. musculus,Yes,1.0,No,Yes,Yes,No,No
+3,Aho2019displacement,PRO-seq,H. sapiens,Yes,1.0,No,Yes,Yes,No,No
+4,Akulenko2018transcriptional,GRO-seq,D. melanogaster,Yes,3.0,No,No,No,No,Yes
+5,Alexander2019imprinted,PRO-seq,M. musculus,No,2.0,No,No,No,No,No
+6,Alhusini2017genomewide,GRO-seq,S. cerevisiae,Yes,4.5,No,No,No,No,No
+7,Allen2014global,GRO-seq,H. sapiens,Yes,3.0,No,No,No,No,Yes
+8,Anderson2020defining,PRO-seq,M. musculus,Yes,3.0,No,No,No,No,No
+9,Andersson2014nuclear,GRO-seq,H. sapiens,Yes,1.0,No,No,No,No,Yes
+10,Andrade2015dna,other,H. sapiens,Yes,2.5,No,No,No,No,No
+11,Andrysik2017identification,GRO-seq,H. sapiens,Yes,1.0,No,Yes,Yes,No,Yes
+12,Aoi2020nelf,"PRO-seq, PRO-cap",H. sapiens,Yes,2.0,No,No,Yes,No,No
+13,Aprile-garcia2019nascent,PRO-seq,H. sapiens,Yes,2.5,No,No,Yes,No,No
+14,Ba2020ctcf,GRO-seq,M. musculus,Yes,1.0,No,No,Yes,Yes,Yes
+15,Bahat2019targeting,GRO-seq,H. sapiens,Yes,2.0,No,Yes,No,No,Yes
+16,Barbieri2020rapid,other,H. sapiens,Yes,4.0,No,Yes,No,No,No
+17,Barucci2020small,PRO-seq,C. elegans,Yes,3.0,No,Yes,No,No,Yes
+18,Beckedorff2020human,PRO-seq,H. sapiens,Yes,1.0,Yes,Yes,Yes,No,Yes
+19,Bi2020enhancer,GRO-seq,H. sapiens,Yes,2.0,Yes,Yes,Yes,No,No
+20,Birkenheuer2018herpes,GRO-seq,H. sapiens,Yes,1.0,No,Yes,No,No,No
+21,Birkenheuer2020rna,PRO-seq,H. sapiens,Yes,1.0,No,No,No,No,No
+22,Blumberg2021characterizing,PRO-seq,H. sapiens,Yes,1.0,No,Yes,No,No,No
+23,Boija2017cbp,PRO-seq,D. melanogaster,Yes,3.5,No,No,Yes,No,Yes
+24,Bonelt2019precocious,GRO-seq,M. musculus,Yes,2.0,Yes,Yes,Yes,No,No
+25,Booth2016divergence,"PRO-cap, PRO-seq","S. cerevisiae, S. pombe",Yes,4.0,No,Yes,No,No,No
+26,Booth2018cdk9,PRO-seq,S. pombe,Yes,4.0,No,No,No,No,No
+27,Bouvyliivrand2017analysis,GRO-seq,H. sapiens,Yes,2.0,No,No,No,No,No
+28,Boxer2020mecp2,PRO-seq,M. musculus,Yes,2.0,No,Yes,Yes,Yes,Yes
+29,Busslinger2017cohesin,GRO-seq,M. musculus,Yes,4.0,No,Yes,Yes,No,No
+30,Cardamone2018mitochondrial,GRO-seq,M. musculus,Yes,3.5,No,Yes,Yes,No,No
+31,Cecere2013zfp1,GRO-seq,C. elegans,Yes,4.0,No,No,No,No,No
+32,Cecere2014global,GRO-seq,C. elegans,Yes,4.0,No,No,No,No,No
+33,Chen2014gene,GRO-seq,H. sapiens,Yes,3.0,No,No,Yes,No,No
+34,Chen2015paf1,"other, GRO-seq",H. sapiens,Yes,2.0,No,Yes,Yes,No,No
+35,Chen2016cutoff,GRO-seq,D. melanogaster,Yes,5.0,No,Yes,Yes,No,No
+36,Chen2017rchip,GRO-seq,H. sapiens,Yes,4.0,No,No,Yes,No,No
+37,Chen2018augmented,GRO-seq,H. sapiens,Yes,3.0,No,No,Yes,No,No
+38,Chen2018rna,GRO-seq,M. musculus,Yes,4.5,No,No,No,No,Yes
+39,Chivu2020unpublished,ChRO-seq,"H. sapiens, E. caballus",No,0.0,Yes,No,Yes,No,Yes
+40,Chu2018chromatin,"ChRO-seq, other, PRO-seq",H. sapiens,Yes,1.0,No,No,No,No,No
+41,Compagno2017phosphatidylinositol,GRO-seq,M. musculus,Yes,1.5,No,No,No,No,Yes
+42,Core2008nascent,GRO-seq,H. sapiens,Yes,4.0,No,No,No,No,No
+43,Core2012defining,GRO-seq,D. melanogaster,Yes,3.0,No,No,Yes,No,No
+44,Core2014analysis,"GRO-cap, GRO-seq, PRO-seq",H. sapiens,Yes,3.5,No,No,No,No,No
+45,Cosby2021recurrent,PRO-seq,M. velifer,Yes,4.0,No,No,Yes,No,No
+46,Cuartero2020control,GRO-seq,M. musculus,Yes,3.0,Yes,Yes,Yes,Yes,No
+47,Czimmerer2018transcription,GRO-seq,M. musculus,Yes,4.0,Yes,Yes,Yes,No,No
+48,Dai2020loop,GRO-seq,M. musculus,Yes,1.0,No,No,Yes,Yes,Yes
+49,Daniel2018nuclear,GRO-seq,M. musculus,Yes,3.0,Yes,Yes,Yes,No,No
+50,Danko2013signaling,GRO-seq,H. sapiens,Yes,2.0,No,No,No,No,No
+51,Danko2015identification,PRO-seq,H. sapiens,Yes,3.0,No,No,No,No,No
+52,Danko2018dynamic,PRO-seq,"H. sapiens, M. mulatta, M. musculus, P. troglodytes, R. norvegicus",Yes,3.0,No,No,No,No,No
+53,Delgado-benito2018chromatin,GRO-seq,M. musculus,Yes,3.0,No,Yes,Yes,No,No
+54,Dorighi2017mll3,GRO-seq,M. musculus,Yes,4.0,Yes,Yes,Yes,No,Yes
+55,Douillet2020uncoupling,PRO-seq,M. musculus,Yes,1.0,No,Yes,Yes,No,Yes
+56,Duarte2016transcription,PRO-seq,D. melanogaster,Yes,3.0,No,Yes,No,No,No
+57,Dukler2017nascent,PRO-seq,H. sapiens,Yes,1.0,No,No,No,No,No
+58,Duttke2015human,"GRO-seq, GRO-cap",H. sapiens,Yes,4.0,No,No,No,No,No
+59,Duttke2017unpublished,"GRO-seq, GRO-cap",D. melanogaster,No,3.5,No,No,No,No,No
+60,Elkon2015myc,GRO-seq,H. sapiens,Yes,3.0,No,Yes,No,No,Yes
+61,Elrod2019integrator,PRO-seq,D. melanogaster,Yes,3.0,Yes,Yes,Yes,No,No
+62,Emmett2017histone,GRO-seq,M. musculus,Yes,3.0,No,Yes,Yes,No,No
+63,Engreitz2016local,PRO-seq,M. musculus,Yes,2.0,Yes,Yes,Yes,No,No
+64,Erhard2015nascent,GRO-seq,Z. mays,Yes,2.0,No,No,No,No,No
+65,Escoubet-lozach2011mechanisms,GRO-seq,M. musculus,Yes,4.0,No,Yes,Yes,No,No
+66,Esousa2019kinetics,PRO-seq,M. musculus,Yes,1.0,No,Yes,No,No,No
+67,Estaras2015smad,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+68,Etchegaray2019histone,PRO-seq,M. musculus,Yes,1.0,No,No,Yes,No,Yes
+69,Fan2020drb,"PRO-seq, other",H. sapiens,Yes,1.0,No,Yes,Yes,No,Yes
+70,Fang2014circadian,GRO-seq,M. musculus,Yes,1.5,No,No,Yes,No,Yes
+71,Fant2020tfiid,PRO-seq,"D. melanogaster, H. sapiens",Yes,3.5,No,No,No,No,No
+72,Fei2018ndf,GRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,No
+73,Fleischer2017dna,GRO-seq,H. sapiens,Yes,3.5,No,No,No,No,Yes
+74,Flynn20167skbaf,GRO-seq,M. musculus,Yes,2.0,Yes,No,Yes,No,Yes
+75,Fong2014pre,GRO-seq,H. sapiens,Yes,5.0,No,Yes,No,No,No
+76,Fong2017rna,NET-seq,H. sapiens,Yes,2.5,No,No,Yes,No,No
+77,Fonseca2019diverse,GRO-seq,M. musculus,Yes,3.5,No,Yes,Yes,No,No
+78,Franco2015tnfalpha,GRO-seq,H. sapiens,Yes,1.0,No,No,Yes,No,No
+79,Franco2018enhancer,GRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,No
+80,Fuda2012fcp1,GRO-seq,D. melanogaster,Yes,4.5,No,No,No,No,No
+81,Fuda2015gaga,GRO-seq,D. melanogaster,Yes,5.0,No,No,Yes,No,Yes
+82,Galbraith2013hif1a,GRO-seq,H. sapiens,Yes,4.0,No,No,Yes,No,Yes
+83,Gally2020gain,PRO-seq,H. sapiens,Yes,2.0,Yes,No,No,No,Yes
+84,Gao2017thyroid,GRO-seq,H. sapiens,Yes,4.0,No,Yes,Yes,No,No
+85,Gao2018jmjd6,GRO-seq,H. sapiens,Yes,3.0,No,Yes,Yes,No,No
+86,Gardini2014integrator,GRO-seq,H. sapiens,Yes,3.0,No,Yes,Yes,No,No
+87,Gibson2016chemical,GRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,Yes
+88,Godfrey2017mll,other,H. sapiens,Yes,1.0,No,No,Yes,Yes,No
+89,Guan2018diet,GRO-seq,M. musculus,Yes,4.0,No,No,Yes,No,No
+90,Hah2011rapid,GRO-seq,H. sapiens,Yes,3.0,No,No,No,No,No
+91,Hah2013enhancer,GRO-seq,H. sapiens,Yes,2.0,No,No,No,No,No
+92,Hah2015inflammation,GRO-seq,M. musculus,Yes,1.5,No,No,No,No,No
+93,Harman2021invivo,GRO-seq,M. musculus,Yes,1.5,Yes,Yes,No,Yes,No
+94,Heinaniemi2016transcription,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+95,Heinz2013effect,GRO-seq,M. musculus,Yes,2.0,No,No,Yes,No,Yes
+96,Herold2019recruitment,GRO-seq,H. sapiens,Yes,4.0,No,Yes,Yes,No,Yes
+97,Hetzel2016nascent,"GRO-seq, GRO-cap",A. thaliana,Yes,3.0,No,Yes,No,No,No
+98,Hong2017dissociation,GRO-seq,M. musculus,Yes,1.5,No,Yes,Yes,No,No
+99,Horibata2018erpositive,PRO-seq,H. sapiens,Yes,1.0,No,No,No,No,No
+100,Hou2019paf1c,PRO-seq,M. musculus,Yes,1.0,Yes,Yes,Yes,No,Yes
+101,Hu2012dicer,GRO-seq,H. sapiens,Yes,2.5,No,Yes,Yes,No,Yes
+102,Huang2020integrator,PRO-seq,D. melanogaster,Yes,3.0,No,Yes,Yes,No,No
+103,Ikegami2020phosphorylated,GRO-seq,H. sapiens,Yes,1.0,Yes,Yes,Yes,No,No
+104,Illingworth2016polycomb,GRO-seq,M. musculus,Yes,3.5,No,No,Yes,No,Yes
+105,Incarnato2017vivo,other,E. coli,Yes,4.0,No,Yes,No,No,Yes
+106,Jaeger2020selective,"PRO-seq, other",H. sapiens,Yes,1.0,No,Yes,Yes,Yes,Yes
+107,Jager2016nuclear,GRO-seq,M. musculus,Yes,2.0,No,No,Yes,No,Yes
+108,Ji2011transcriptional,GRO-seq,M. musculus,Yes,2.0,No,No,No,No,No
+109,Ji2013sr,GRO-seq,M. musculus,Yes,4.0,No,No,Yes,No,No
+110,Jiang2018multi,GRO-seq,H. sapiens,Yes,1.5,No,Yes,No,No,Yes
+111,Jin2013high,GRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,Yes,No
+112,Jin2014chem,GRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,No
+113,Johnson2017biotin,GRO-seq,M. musculus,Yes,2.0,No,Yes,No,No,No
+114,Johnston2020nascent,PRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,Yes
+115,Jones2023unpublished,PRO-seq,H. sapiens,No,3.0,No,No,No,No,No
+116,Jonkers2014genome,GRO-seq,M. musculus,Yes,2.0,No,No,No,No,No
+117,Judd2020unpublished,"other, PRO-seq",H. sapiens,No,3.5,No,No,No,No,No
+118,Judd2021pioneer,PRO-seq,D. melanogaster,Yes,3.0,Yes,Yes,Yes,No,Yes
+119,Kaikkonen2013remodeling,GRO-seq,M. musculus,Yes,3.0,No,No,Yes,No,No
+120,Kaikkonen2014control,GRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,Yes,No
+121,Kaikkonen2017genome,GRO-seq,S. scrofa,Yes,4.0,No,No,No,No,No
+122,Kantidakis2016mutation,GRO-seq,M. musculus,Yes,1.0,No,No,Yes,No,No
+123,Kelly2020unpublished,PRO-seq,M. musculus,No,2.0,No,No,No,No,Yes
+124,Khodor2011nascent,other,D. melanogaster,Yes,3.0,No,Yes,No,No,No
+125,Kim2018pluripotency,PRO-cap,M. musculus,Yes,4.5,Yes,Yes,Yes,No,Yes
+126,Kloetgen2020three,GRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,Yes,Yes
+127,Komarov2020epigenetic,GRO-seq,D. melanogaster,Yes,3.0,No,Yes,No,No,No
+128,Korkmaz2019crispr,GRO-seq,H. sapiens,Yes,1.0,No,Yes,Yes,No,No
+129,Kourtis2018oncogenic,GRO-seq,H. sapiens,Yes,3.0,No,Yes,Yes,No,Yes
+130,Kriaucionis2019unpublished,"PRO-seq, PRO-cap",H. sapiens,No,2.0,No,Yes,No,No,Yes
+131,Kristjansdottir2020population,"PRO-seq, PRO-cap",H. sapiens,Yes,4.0,No,No,No,No,No
+132,Kruesi2013condensin,"GRO-seq, GRO-cap",C. elegans,Yes,3.5,No,No,Yes,No,No
+133,Kuosmanen2018nrf2,GRO-seq,H. sapiens,Yes,2.5,No,Yes,No,No,Yes
+134,Kwak2013precise,"PRO-seq, PRO-cap",D. melanogaster,Yes,4.0,No,No,No,No,No
+135,Kwon2017locus,GRO-seq,M. musculus,Yes,3.0,No,Yes,Yes,No,No
+136,Lai2020directed,PRO-seq,M. musculus,Yes,1.0,No,Yes,No,No,No
+137,Laitem2015cdk9,GRO-seq,H. sapiens,Yes,3.0,No,No,No,No,No
+138,Lam2013rev,"GRO-cap, GRO-seq",M. musculus,Yes,3.5,No,No,Yes,No,No
+139,Larschan2011x,GRO-seq,D. melanogaster,Yes,3.0,No,No,No,No,No
+140,Le2013mapping,GRO-seq,H. sapiens,Yes,3.0,No,No,Yes,No,No
+141,Leroy2019ledgf,PRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,No
+142,Leveille2015genome,GRO-seq,H. sapiens,Yes,3.0,No,Yes,Yes,Yes,Yes
+143,Li2013functional,GRO-seq,H. sapiens,Yes,1.0,No,No,Yes,No,Yes
+144,Li2013ncor,GRO-seq,M. musculus,Yes,5.0,No,No,Yes,No,No
+145,Li2015condensin,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+146,Li2017grid,GRO-seq,H. sapiens,Yes,4.0,No,No,No,No,Yes
+147,Li2018lncrna,GRO-seq,H. sapiens,Yes,3.0,No,Yes,No,No,Yes
+148,Li2020human,PRO-seq,H. sapiens,Yes,3.0,No,No,No,No,No
+149,Li2020signalosome,PRO-seq,R. norvegicus,Yes,4.0,No,No,Yes,No,No
+150,Li2021comprehensive,GRO-seq,H. sapiens,Yes,1.5,No,Yes,No,No,No
+151,Liang2018targeting,PRO-seq,H. sapiens,Yes,1.0,No,Yes,Yes,No,Yes
+152,Lin2012global,GRO-seq,M. musculus,Yes,2.5,No,No,Yes,Yes,No
+153,Link2018analysis,"GRO-seq, GRO-cap",M. musculus,Yes,3.0,Yes,Yes,Yes,Yes,Yes
+154,Linnakuosmanen2020nrf2,GRO-seq,H. sapiens,Yes,2.0,No,Yes,No,No,Yes
+155,Liu2013brd4,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+156,Liu2014enhancer,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+157,Liu2017dynamic,GRO-seq,H. sapiens,Yes,3.0,No,No,No,No,No
+158,Liu2017identification,PRO-seq,H. sapiens,Yes,2.0,No,No,No,No,No
+159,Liu2017transcriptional,GRO-seq,H. sapiens,Yes,1.0,No,Yes,Yes,No,Yes
+160,Liu2018arabidopsis,GRO-seq,A. thaliana,Yes,4.0,No,Yes,Yes,No,No
+161,Liu2018rna-directed,GRO-seq,A. thaliana,Yes,2.0,No,Yes,Yes,No,No
+162,Liu2020immediate,GRO-seq,A. thaliana,Yes,4.0,No,Yes,No,No,No
+163,Liu2021transcription,PRO-seq,H. sapiens,Yes,1.0,Yes,No,Yes,No,Yes
+164,Lloret-llinares2018rna,PRO-seq,M. musculus,Yes,1.0,No,Yes,No,No,Yes
+165,Lozano2018rna,PRO-seq,"Z. mays, M. esculenta",No,2.5,No,No,No,No,No
+166,Lu2017nascent,other,P. falciparum,Yes,4.0,No,No,Yes,No,No
+167,Luo2014dynamic,GRO-seq,H. sapiens,Yes,1.0,No,No,Yes,No,No
+168,Ma2020super,GRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,Yes
+169,Magnuson2015identifying,other,H. sapiens,Yes,3.0,No,No,No,No,No
+170,Mahat2016mammalian,PRO-seq,M. musculus,Yes,1.0,No,No,Yes,No,No
+171,Malinen2017crosstalk,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+172,Marazzi2012suppression,GRO-seq,H. sapiens,Yes,3.0,No,Yes,Yes,No,No
+173,Mayer2015native,NET-seq,H. sapiens,Yes,4.0,No,Yes,No,No,No
+174,Mckinlay2011genome,PRO-seq,S. cerevisiae,Yes,5.0,No,Yes,No,No,No
+175,Meng2014convergent,GRO-seq,"M. musculus, H. sapiens",Yes,4.0,No,No,Yes,No,No
+176,Meyerswallen2017xx,ChRO-seq,C. lupus familiaris,Yes,3.0,No,Yes,No,No,Yes
+177,Miller2015senataxin,GRO-seq,H. sapiens,Yes,5.0,No,Yes,No,No,No
+178,Min2011regulating,GRO-seq,M. musculus,Yes,5.0,No,No,No,No,No
+179,Mohn2014rhino,GRO-seq,D. melanogaster,Yes,4.5,No,Yes,Yes,No,Yes
+180,Moreau2018transcriptional,GRO-seq,H. sapiens,Yes,2.0,No,Yes,No,No,No
+181,Mukai2020chromatin,ChRO-seq,C. lupus familiaris,Yes,4.0,No,No,No,No,No
+182,Murakami2017dynamic,GRO-seq,H. sapiens,Yes,3.0,No,No,Yes,No,No
+183,Nair2019phase,GRO-seq,"H. sapiens, M. musculus",Yes,1.0,Yes,No,Yes,Yes,No
+184,Nelson2018ppar,GRO-seq,M. musculus,Yes,2.0,No,Yes,Yes,No,No
+185,Ngoc2017human,GRO-seq,H. sapiens,Yes,3.0,No,No,No,No,No
+186,Nguyen2020dichotomous,GRO-seq,M. musculus,Yes,3.0,No,Yes,Yes,No,No
+187,Nilson2017oxidative,PRO-seq,H. sapiens,Yes,1.5,No,No,Yes,No,No
+188,Niskanen2015global,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+189,Niskanen2018endothelial,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,Yes
+190,Nojima2015mammalian,"NET-seq, other",H. sapiens,Yes,2.0,No,Yes,No,No,No
+191,Oh2021enhancer,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,Yes,No
+192,Oittinen2017polycomb,GRO-seq,M. musculus,Yes,2.0,No,No,Yes,No,No
+193,Orioli2016human,other,H. sapiens,Yes,4.5,No,No,Yes,No,Yes
+194,Parida2019nucleotide,"PRO-seq, PRO-cap",H. sapiens,Yes,3.0,No,No,No,No,No
+195,Parikh2018critical,GRO-seq,D. melanogaster,Yes,3.0,No,Yes,No,No,Yes
+196,Park2020global,GRO-seq,H. sapiens,Yes,1.5,No,No,Yes,Yes,No
+197,Parua2018cdk9-pp1,PRO-seq,S. pombe,Yes,4.0,No,No,Yes,No,No
+198,Patel2020robust,PRO-seq,H. sapiens,Yes,2.0,No,Yes,No,No,Yes
+199,Perreault2019epigenetic,PRO-seq,H. sapiens,Yes,3.5,No,No,Yes,No,Yes
+200,Phanstiel2017static,PRO-seq,H. sapiens,Yes,4.0,Yes,Yes,Yes,Yes,No
+201,Puc2015ligand,"GRO-seq, PRO-cap",H. sapiens,Yes,2.5,No,No,Yes,No,No
+202,Rahnamoun2017mutant,GRO-seq,H. sapiens,Yes,1.0,No,Yes,Yes,No,No
+203,Rao2017cohesin,PRO-seq,H. sapiens,Yes,1.0,No,No,Yes,Yes,No
+204,Rozhkov2013multiple,GRO-seq,D. melanogaster,Yes,3.0,No,Yes,Yes,No,No
+205,Salony2016akt,GRO-seq,H. sapiens,Yes,5.0,No,Yes,No,No,Yes
+206,Santoriello2020rna,PRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,Yes
+207,Saponaro2014recql5,GRO-seq,H. sapiens,Yes,3.5,No,No,Yes,No,No
+208,Sasse2019nascent,GRO-seq,H. sapiens,Yes,4.0,No,No,Yes,No,No
+209,Sathyan2019improved,PRO-seq,H. sapiens,Yes,3.0,No,No,No,No,No
+210,Saunders2013extensive,GRO-seq,D. melanogaster,Yes,5.0,No,No,No,No,No
+211,Schaaf2013genome,PRO-seq,D. melanogaster,Yes,3.0,No,No,No,No,Yes
+212,Schaukowitch2017intrinsic,GRO-seq,M. musculus,Yes,3.0,No,Yes,No,No,No
+213,Schick2021acute,PRO-seq,H. sapiens,Yes,1.0,Yes,Yes,Yes,No,No
+214,Schoeberl2012biased,GRO-seq,T. thermophila,Yes,5.0,No,Yes,No,No,No
+215,Sen2019histone,PRO-seq,H. sapiens,Yes,2.0,No,Yes,No,No,Yes
+216,Sendinc2019pcif1,"PRO-seq, PRO-cap",H. sapiens,Yes,1.0,No,No,No,No,Yes
+217,Shamie2020unpublished,"GRO-seq, GRO-cap",C. griseus,No,4.0,Yes,Yes,No,No,No
+218,Sheridan2019widespread,"NET-seq, other, GRO-seq",H. sapiens,Yes,3.0,No,No,Yes,No,No
+219,Sienski2012transcriptional,GRO-seq,D. melanogaster,Yes,3.5,No,Yes,Yes,No,Yes
+220,Sigova2013divergent,GRO-seq,H. sapiens,Yes,1.0,No,Yes,No,No,Yes
+221,Sigova2015transcription,GRO-seq,M. musculus,Yes,4.0,No,Yes,Yes,No,Yes
+222,Skowronskakrawczyk2014required,GRO-seq,R. norvegicus,Yes,2.0,No,No,Yes,No,No
+223,Slobodin2017transcription,GRO-seq,H. sapiens,Yes,2.5,No,Yes,No,No,Yes
+224,Smith2021peppro,PRO-seq,H. sapiens,Yes,1.0,No,No,No,No,No
+225,Soccio2015genetic,GRO-seq,M. musculus,Yes,3.0,No,Yes,Yes,No,No
+226,Steinparzer2019transcriptional,"PRO-seq, GRO-seq","H. sapiens, M. musculus",Yes,3.0,No,Yes,No,No,No
+227,Stender2017structural,GRO-seq,H. sapiens,Yes,3.5,No,Yes,Yes,No,No
+228,Stengel2019histone,PRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,No
+229,Stengel2020definition,PRO-seq,H. sapiens,Yes,1.0,No,Yes,Yes,No,Yes
+230,Step2014antidiabetic,GRO-seq,M. musculus,Yes,2.5,No,No,No,No,Yes
+231,Strikoudis2016regulation,GRO-seq,M. musculus,Yes,3.0,No,Yes,Yes,No,No
+232,Sumida2018ultra,other,H. sapiens,No,5.0,No,Yes,Yes,No,Yes
+233,Sun2017enhancer,GRO-seq,M. musculus,No,1.0,No,Yes,No,No,No
+234,Takahashi2020role,PRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,No
+235,Tan2016stress,GRO-seq,H. sapiens,Yes,4.0,No,Yes,Yes,No,Yes
+236,Tan2018dismissal,"PRO-seq, GRO-seq",H. sapiens,Yes,2.0,No,No,Yes,Yes,No
+237,Tastemel2017transcription,GRO-seq,M. musculus,Yes,3.0,Yes,No,No,No,No
+238,Telese2015lrp8,GRO-seq,M. musculus,Yes,2.5,No,Yes,Yes,Yes,No
+239,Tena2020induction,GRO-seq,M. musculus,Yes,1.0,No,No,No,No,Yes
+240,Teppo2016genome,GRO-seq,H. sapiens,Yes,2.0,No,No,No,No,No
+241,Thomas2019interaction,PRO-seq,H. sapiens,Yes,2.0,No,Yes,Yes,No,No
+242,Tome2018single,other,"M. musculus, H. sapiens",Yes,3.0,No,No,No,No,No
+243,Toropainen2016global,GRO-seq,H. sapiens,Yes,1.0,No,No,Yes,No,No
+244,Trizzino2018tumor,GRO-seq,H. sapiens,Yes,4.0,Yes,Yes,Yes,No,No
+245,Ueberschar2019ben,PRO-seq,D. melanogaster,Yes,4.0,No,Yes,Yes,No,Yes
+246,Vaid2020release,PRO-seq,D. melanogaster,Yes,3.0,Yes,Yes,Yes,No,No
+247,Veloso2013genome-wide,other,H. sapiens,Yes,1.5,No,No,No,No,No
+248,Vian2018energetics,"other, GRO-seq",M. musculus,Yes,3.0,No,Yes,Yes,Yes,Yes
+249,Vihervaara2017transcriptional,PRO-seq,H. sapiens,Yes,1.5,No,No,Yes,No,No
+250,Vihervaara2021stress,PRO-seq,"M. musculus, H. sapiens",Yes,4.0,Yes,No,No,No,No
+251,Viiri2019extensive,GRO-seq,H. sapiens,Yes,2.0,No,No,No,No,No
+252,Wan2020h2bg53d,PRO-seq,H. sapiens,Yes,1.0,Yes,Yes,No,No,Yes
+253,Wang2011reprogramming,GRO-seq,H. sapiens,Yes,3.0,No,No,Yes,No,No
+254,Wang2014rna,"PRO-seq, GRO-seq",H. sapiens,Yes,2.0,No,Yes,No,No,Yes
+255,Wang2015epigenetic,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+256,Wang2015lsd1n,GRO-seq,M. musculus,Yes,3.0,No,Yes,Yes,No,No
+257,Wang2015molecular,GRO-seq,M. musculus,Yes,3.0,No,No,No,No,No
+258,Wang2017cell,GRO-seq,M. musculus,Yes,4.0,No,No,No,No,Yes
+259,Wang2018nascent,PRO-seq,M. musculus,Yes,1.0,No,No,No,No,No
+260,Wang2019identification,PRO-seq,H. sapiens,Yes,1.0,Yes,No,No,No,No
+261,Wang2020increased,GRO-seq,H. sapiens,Yes,1.0,No,No,No,No,Yes
+262,Wang2020proapoptotic,GRO-seq,H. sapiens,Yes,1.0,No,No,Yes,No,No
+263,Wei2016long,GRO-seq,M. musculus,Yes,2.0,No,No,No,No,Yes
+264,Wei2016rbfox2,GRO-seq,M. musculus,Yes,3.0,No,No,Yes,No,Yes
+265,Weissmiller2019inhibition,PRO-seq,H. sapiens,Yes,2.0,Yes,No,Yes,No,No
+266,Williams2015pausing,GRO-seq,M. musculus,Yes,2.0,No,Yes,No,No,Yes
+267,Williamson2017uv,GRO-seq,H. sapiens,Yes,1.0,No,Yes,No,No,Yes
+268,Woo2018ted,PRO-seq,H. sapiens,Yes,1.0,No,Yes,No,No,Yes
+269,Wu2017indentifying,GRO-seq,M. musculus,Yes,4.5,No,No,No,No,No
+270,Xiao2019pervasive,GRO-seq,H. sapiens,Yes,4.0,No,No,Yes,Yes,No
+271,Yang2013lncrna,GRO-seq,H. sapiens,Yes,1.5,No,No,Yes,No,Yes
+272,Yang2017glucocorticoid,GRO-seq,H. sapiens,Yes,2.0,No,No,Yes,No,No
+273,Yu2015panoramix,GRO-seq,D. melanogaster,Yes,5.0,No,Yes,Yes,No,No
+274,Yu2020negative,PRO-seq,M. musculus,Yes,2.0,No,Yes,Yes,No,No
+275,Zhang2015enhancer,GRO-seq,M. musculus,Yes,2.0,No,No,Yes,No,No
+276,Zhang2016regulation,GRO-seq,H. sapiens,Yes,3.0,No,No,Yes,No,No
+277,Zhang2017hepatic,GRO-seq,M. musculus,Yes,2.5,No,No,Yes,No,Yes
+278,Zhang2018timing,other,H. sapiens,No,2.0,No,No,No,No,No
+279,Zhang2019arerg,GRO-seq,H. sapiens,Yes,2.0,No,Yes,No,Yes,No
+280,Zhang2019fundamental,GRO-seq,M. musculus,Yes,1.0,No,No,Yes,Yes,Yes
+281,Zhang2020bcatenin,GRO-seq,M. musculus,Yes,5.0,Yes,Yes,No,No,No
+282,Zhang2021physiological,GRO-seq,M. musculus,Yes,1.0,No,No,No,Yes,Yes
+283,Zhao2016high,PRO-seq,H. sapiens,Yes,1.5,No,Yes,No,No,Yes
+284,Zhao2019myod,PRO-seq,M. musculus,Yes,2.0,No,Yes,No,No,No
+285,Zhu2017comprehensive,GRO-seq,M. musculus,Yes,3.5,No,Yes,Yes,Yes,Yes
+286,Zhu2018rna,"NET-seq, GRO-seq",A. thaliana,Yes,3.0,No,Yes,No,No,No
+287,Zhu2019non,GRO-seq,H. sapiens,Yes,1.5,No,Yes,Yes,No,No
+288,Zhu2021calcium,GRO-seq,M. musculus,Yes,3.5,Yes,No,Yes,Yes,No

datasets.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:afc02ef390d4ad78d36a00da546b17c961be07daded8be4743a311a69ef111cc
+size 13016

scrap.py

@@ -0,0 +1,42 @@
+# -*- coding: utf-8 -*-
+"""Untitled3.ipynb
+
+Automatically generated by Colaboratory.
+
+Original file is located at
+    https://colab.research.google.com/drive/1OPk27uLuoRSbYWcNdKG0Qtq0Ffb9RrcT
+"""
+
+import requests
+import pandas as pd
+
+urls = ['https://nascent.colorado.edu/samples/all_samples','https://nascent.colorado.edu/datasets']
+
+for url in urls:
+  html = requests.get(url).content
+  dfs = pd.read_html(html)
+  # Make the first line header and string
+  dfs[0].columns = dfs[0].iloc[0]
+  dfs[0] = dfs[0].iloc[1:].astype(str)
+  # pretty print dfs
+  for i, df in enumerate(dfs):
+    print(f"{i}: {df.shape}")
+    print(df.head())
+  # Write to parquet file
+  dfs[0].to_parquet(f"{url.split('/')[-1]}.parquet")
+  # Make a csv version while we're here
+  dfs[0].to_csv(f"{url.split('/')[-1]}.csv")
+
+# Scrap this website
+# https://nascent.colorado.edu/
+# TODO once we pick out some samples of interest
+import requests
+from bs4 import BeautifulSoup
+
+response = requests.get('https://nascent.colorado.edu/samples/SRZ7741175')
+soup = BeautifulSoup(response.content, 'html.parser')
+
+bed_files = soup.find_all('a', href=re.compile('.bed$'))
+
+for bed_file in bed_files:
+  print(bed_file['href'])