In this section, we investigate overlaps of peaks with the different genomic features.

TKO/D3 peaks

Let’s look first at those peaks that are lost in TKO with respect of D3.

The total number of peaks is 41215 of which only 393 are lost in TKO when compared to D3 (FDR < 0.05, Log2FC < -1).

Overlap with gene features (a.k.a genes)

A summary barplot is shown below, the categories are somehow selected for:

gencode class frequency our class
miRNA 1 smallRNA
snoRNA 1 smallRNA
bidirectional_promoter_lncRNA 2 lncRNA
snRNA 2 smallRNA
TEC 2 other
transcribed_unitary_pseudogene 2 pseudo
unprocessed_pseudogene 2 pseudo
transcribed_processed_pseudogene 3 pseudo
sense_overlapping 4 other
misc_RNA 5 other
sense_intronic 6 other
processed_pseudogene 7 pseudo
processed_transcript 10 other
transcribed_unprocessed_pseudogene 10 pseudo
antisense 22 other
lincRNA 33 lncRNA
protein_coding 238 coding

Among the protein coding genes, there are 46 ZNF genes (of a total of 646 annotated in the genome).

Testing for enrichment of ZNFs in peaks.

##          ZNF no.ZNF
## yes.peak  46    304
## no.peak  469  19425

We apply Fisher Exact test where the H0 is that the proportion of ZNFs found in peaks is the same as the proportion found in the general pool of genes vs the alternative HA which states that the proportion of ZNFs in peaks is greater than that of the general pool of genes.

## 
##  Fisher's Exact Test for Count Data
## 
## data:  contingency.table
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  4.685079      Inf
## sample estimates:
## odds ratio 
##   6.265804

The P-value indicates that we reject the H0 in the favor of HA.

Protein coding overlaping peaks

chrom start end gene_id gene_name
chr3 100749156 100993515 ENSG00000154175.16 ABI3BP
chr7 92131774 92245924 ENSG00000285953.1 AC000120.3
chr19 57487718 57505381 ENSG00000268107.5 AC003005.1
chr19 57682045 57753575 ENSG00000269026.2 AC003006.1
chr19 57437970 57477536 ENSG00000268163.1 AC004076.1
chr12 4649101 4774184 ENSG00000255639.3 AC005833.1
chr12 4273762 4405490 ENSG00000285901.1 AC008012.1
chr19 57876765 57916591 ENSG00000269476.1 AC010326.2
chr19 52880663 52962768 ENSG00000283088.1 AC010487.3
chr16 71447600 71489311 ENSG00000261611.6 AC010547.4
chr3 28349178 29767537 ENSG00000283563.1 AC098650.1
chr3 113361901 113515151 ENSG00000285943.1 AC112128.1
chr1 75724347 75787575 ENSG00000117054.13 ACADM
chr6 135283532 135497776 ENSG00000135541.20 AHI1
chr10 38094368 38360098 ENSG00000283930.1 AL117339.5
chr9 21802636 22032986 ENSG00000264545.1 AL359922.1
chr2 73385758 73610793 ENSG00000116127.17 ALMS1
chr2 201288271 201357398 ENSG00000155749.12 ALS2CR12
chr5 140401814 140539856 ENSG00000131503.20 ANKHD1
chr5 140401908 140549569 ENSG00000254996.5 ANKHD1-EIF4EBP3
chr7 92246234 92401384 ENSG00000001629.9 ANKIB1
chr18 9136228 9285985 ENSG00000101745.16 ANKRD12
chr17 60443149 60526219 ENSG00000062725.9 APPBP2
chr12 105173296 105236238 ENSG00000136044.11 APPL2
chr4 152779937 152918463 ENSG00000164144.15 ARFIP1
chr10 50739318 50816495 ENSG00000204147.10 ASAH2B
chr1 197084128 197146694 ENSG00000066279.17 ASPM
chr5 81972025 82276857 ENSG00000152348.15 ATG10
chr11 108222484 108369102 ENSG00000149311.18 ATM
chr3 142449235 142578826 ENSG00000175054.14 ATR
chr17 82942155 83051810 ENSG00000175711.8 B3GNTL1
chr11 27654893 27722058 ENSG00000176697.18 BDNF
chr13 32315474 32400266 ENSG00000139618.14 BRCA2
chr11 108308519 108467531 ENSG00000166323.12 C11orf65
chr2 27537386 27582721 ENSG00000221843.4 C2orf16
chr2 189879609 190203484 ENSG00000187699.10 C2orf88
chr15 44288729 44415758 ENSG00000166734.19 CASC4
chr4 168863770 169010275 ENSG00000145439.11 CBR4
chr2 113437691 113496189 ENSG00000136682.14 CBWD2
chr9 68232003 68300015 ENSG00000196873.15 CBWD3
chr2 196639554 196763490 ENSG00000144395.17 CCDC150
chr13 102729369 102759070 ENSG00000175820.3 CCDC168
chr1 93179919 93278730 ENSG00000122483.17 CCDC18
chr1 169394870 169460669 ENSG00000117477.12 CCDC181
chr10 32446140 32882874 ENSG00000216937.13 CCDC7
chr11 96352769 96389956 ENSG00000149231.13 CCDC82
chr5 134286350 134371047 ENSG00000006837.11 CDKL3
chr2 37201612 37231713 ENSG00000115816.14 CEBPZ
chr2 37196488 37216193 ENSG00000218739.9 CEBPZOS
chr10 93496632 93529092 ENSG00000138180.15 CEP55
chr11 95789965 95832693 ENSG00000166037.10 CEP57
chr3 101723925 101770562 ENSG00000182504.10 CEP97
chr3 113286947 113441610 ENSG00000206530.10 CFAP44
chr2 86503431 86563479 ENSG00000115561.15 CHMP3
chr11 77514936 77637805 ENSG00000074201.8 CLNS1A
chr9 17134982 17503923 ENSG00000044459.14 CNTLN
chr7 43608456 43729717 ENSG00000106603.18 COA1
chr13 39655627 39791665 ENSG00000133103.16 COG6
chrX 108439844 108697545 ENSG00000188153.13 COL4A5
chr1 175944831 176207493 ENSG00000143207.20 COP1
chr2 210477682 210679107 ENSG00000021826.15 CPS1
chr6 83859643 83967424 ENSG00000065615.13 CYB5R4
chr3 98795941 98901689 ENSG00000057019.15 DCBLD2
chr8 90001405 90052092 ENSG00000104325.6 DECR1
chr17 21123364 21193265 ENSG00000109016.17 DHRS7B
chr11 111927144 112022584 ENSG00000150764.13 DIXDC1
chr5 119037772 119249138 ENSG00000172869.14 DMXL1
chr2 195737703 196068812 ENSG00000118997.13 DNAH7
chr18 67506582 67516980 ENSG00000171451.13 DSEL
chr1 212035553 212107400 ENSG00000143476.17 DTL
chr3 108589682 108694846 ENSG00000198919.12 DZIP3
chr17 47323290 47441312 ENSG00000178852.15 EFCAB13
chr5 60873831 60945073 ENSG00000049167.14 ERCC8
chr21 38380027 38661780 ENSG00000157554.18 ERG
chr19 53013921 53016122 ENSG00000269526.1 ERVV-1
chrX 57286706 57489196 ENSG00000165591.6 FAAH2
chr11 59107185 59127410 ENSG00000189057.10 FAM111B
chr5 80487969 80542563 ENSG00000152380.9 FAM151B
chr7 102748971 102809225 ENSG00000222011.8 FAM185A
chr15 49326962 49620931 ENSG00000166262.15 FAM227B
chr4 112145397 112195256 ENSG00000174749.5 FAM241A
chr15 59372693 59523549 ENSG00000157470.11 FAM81A
chr11 72836745 73142261 ENSG00000137478.14 FCHSD2
chr1 59296638 59810647 ENSG00000172456.17 FGGY
chr9 105558130 105641118 ENSG00000106692.14 FKTN
chr15 49155656 49367869 ENSG00000156958.14 GALK2
chr18 35581117 35711834 ENSG00000141429.13 GALNT1
chr14 54842008 54902852 ENSG00000131979.18 GCH1
chr5 151822513 151924842 ENSG00000145888.10 GLRA1
chr9 86026146 86100173 ENSG00000135052.16 GOLM1
chrX 9725346 9786297 ENSG00000101850.12 GPR143
chr10 91409280 91514829 ENSG00000165338.16 HECTD2
chr15 28111040 28322152 ENSG00000128731.16 HERC2
chr2 190189735 190344193 ENSG00000198130.15 HIBCH
chr6 12008762 12164999 ENSG00000095951.16 HIVEP1
chrX 131273506 131578899 ENSG00000147255.18 IGSF1
chr9 5123880 5185668 ENSG00000120210.7 INSL6
chr9 100099256 100301000 ENSG00000119509.12 INVS
chr13 101452593 101720856 ENSG00000198542.13 ITGBL1
chr9 4984390 5128183 ENSG00000096968.13 JAK2
chr11 96389989 96507574 ENSG00000183340.6 JRKL
chrX 53094145 53170914 ENSG00000232593.7 KANTR
chr18 79863668 79900184 ENSG00000178342.4 KCNG2
chr4 20728616 21948799 ENSG00000185774.15 KCNIP4
chr12 280129 389454 ENSG00000073614.12 KDM5A
chr1 35433490 35557950 ENSG00000142687.17 KIAA0319L
chr14 58427385 58551289 ENSG00000100578.14 KIAA0586
chr5 94152966 94618597 ENSG00000185261.14 KIAA0825
chr12 31959370 31993107 ENSG00000174718.11 KIAA1551
chr15 89608789 89655451 ENSG00000166813.14 KIF7
chr1 173714941 173786702 ENSG00000076321.10 KLHL20
chr6 116681187 116741866 ENSG00000196911.10 KPNA5
chrX 46446857 46497422 ENSG00000147121.15 KRBOX4
chr13 108207439 108218368 ENSG00000174405.13 LIG4
chr4 150264531 151015727 ENSG00000198589.11 LRBA
chr1 116111755 116135240 ENSG00000173212.4 MAB21L3
chr1 113390749 113685923 ENSG00000081026.18 MAGI3
chr2 148021011 148516971 ENSG00000204406.13 MBD5
chr6 118813442 118935162 ENSG00000111877.17 MCM9
chr12 27022546 27066343 ENSG00000152944.8 MED21
chr18 21704957 21870957 ENSG00000101752.11 MIB1
chr14 37197913 37552361 ENSG00000151338.18 MIPOL1
chr22 30925130 30968298 ENSG00000133422.12 MORC2
chr9 21802543 21937651 ENSG00000099810.19 MTAP
chr8 120445400 120542133 ENSG00000172167.7 MTBP
chr19 8848844 8981342 ENSG00000181143.15 MUC16
chr15 71822289 72118577 ENSG00000066933.15 MYO9A
chr3 174438573 175810552 ENSG00000177694.15 NAALADL2
chr12 4649095 4694317 ENSG00000139180.10 NDUFA9
chr4 169392857 169612629 ENSG00000137601.16 NEK1
chr2 177227595 177392697 ENSG00000116044.15 NFE2L2
chr3 173396284 174286644 ENSG00000169760.17 NLGN1
chr4 148078762 148444698 ENSG00000151623.14 NR3C2
chr3 31657890 32077580 ENSG00000144645.13 OSBPL10
chr5 38845858 38945596 ENSG00000145623.12 OSMR
chr4 20696282 20752907 ENSG00000163138.18 PACRGL
chr2 61017225 61051990 ENSG00000162928.8 PEX13
chr20 8077251 8968360 ENSG00000182621.17 PLCB1
chr5 55424854 55535050 ENSG00000067113.16 PLPP1
chr11 74171099 74254703 ENSG00000214517.9 PPME1
chr6 57314805 57646849 ENSG00000146143.17 PRIM2
chr7 549197 727650 ENSG00000188191.14 PRKAR1B
chr11 112226365 112269955 ENSG00000150787.7 PTS
chr12 43718993 43758817 ENSG00000129317.14 PUS7L
chr12 9148840 9208370 ENSG00000126838.9 PZP
chr3 120686681 120742993 ENSG00000144840.9 RABL3
chr7 5045821 5069488 ENSG00000146587.17 RBAK
chr7 4983718 5073221 ENSG00000272968.5 RBAK-RBAKDN
chr2 86505668 86721122 ENSG00000249884.8 RNF103-CHMP3
chr1 92298965 92402056 ENSG00000122484.8 RPAP2
chr18 70003031 70205945 ENSG00000176225.13 RTTN
chr3 134065303 134250744 ENSG00000163785.12 RYK
chr13 23328826 23433740 ENSG00000151835.15 SACS
chr7 93099513 93118023 ENSG00000205413.7 SAMD9
chr4 128864921 129093607 ENSG00000151466.11 SCLT1
chr6 107867756 107958189 ENSG00000025796.13 SEC63
chr2 217730 266398 ENSG00000035115.21 SH3YL1
chr15 50182196 50236395 ENSG00000140284.10 SLC27A2
chr10 93893973 93956062 ENSG00000176273.14 SLC35G1
chr12 46183063 46270017 ENSG00000111371.15 SLC38A1
chr3 113442718 113515187 ENSG00000163611.11 SPICE1
chrX 56818298 56995827 ENSG00000204271.12 SPIN3
chr2 9843354 9934416 ENSG00000115750.16 TAF1B
chr5 141260225 141320821 ENSG00000178913.7 TAF7
chr17 82752064 82945922 ENSG00000141556.20 TBCD
chr4 106041599 106321495 ENSG00000145348.16 TBCK
chrX 9463295 9741037 ENSG00000101849.16 TBL1X
chr13 113584721 113641470 ENSG00000198176.12 TFDP1
chr3 141944428 142149544 ENSG00000114126.17 TFDP2
chr2 187464230 187565760 ENSG00000003436.15 TFPI
chr2 43230836 43596046 ENSG00000115970.18 THADA
chr12 4307763 4354593 ENSG00000078237.6 TIGAR
chr5 43444252 43483893 ENSG00000151881.14 TMEM267
chr3 119429500 119468830 ENSG00000176142.12 TMEM39A
chr3 100492619 100577444 ENSG00000181458.10 TMEM45A
chr15 42210452 42273663 ENSG00000103978.15 TMEM87A
chr13 100603927 100675093 ENSG00000125247.15 TMTC4
chr21 44350163 44443081 ENSG00000142185.16 TRPM2
chr2 98997261 99154964 ENSG00000135951.14 TSGA10
chr3 23203020 23591793 ENSG00000182247.9 UBE2E2
chr6 99432379 99521728 ENSG00000123552.17 USP45
chr7 55436056 55572988 ENSG00000154978.12 VOPP1
chr15 61852389 62060473 ENSG00000129003.17 VPS13C
chr7 93232340 93361121 ENSG00000004766.16 VPS50
chr5 37379212 37753435 ENSG00000082068.8 WDR70
chr3 195068279 195271167 ENSG00000173950.15 XXYLT1
chr3 38346760 38421348 ENSG00000093217.10 XYLB
chr3 114314501 115147271 ENSG00000181722.16 ZBTB20
chr3 28349146 28538122 ENSG00000206559.7 ZCWPW2
chr2 206274663 206314438 ENSG00000204186.8 ZDBF2
chr11 19117099 19176422 ENSG00000177054.13 ZDHHC13
chr10 31318495 31529814 ENSG00000148516.21 ZEB1
chr10 134465 254637 ENSG00000015171.19 ZMYND11
chr19 19668796 19683509 ENSG00000181896.11 ZNF101
chr7 64666083 64711582 ENSG00000196247.11 ZNF107
chr19 36214602 36238774 ENSG00000167635.11 ZNF146
chr19 43967862 43998325 ENSG00000204920.10 ZNF155
chr19 53066606 53103436 ENSG00000170949.17 ZNF160
chr9 101398873 101410660 ENSG00000136870.10 ZNF189
chr3 44584888 44648471 ENSG00000186448.14 ZNF197
chr19 57630395 57642779 ENSG00000121417.13 ZNF211
chr19 43951223 43967709 ENSG00000159905.14 ZNF221
chr16 71447597 71463095 ENSG00000167377.18 ZNF23
chr10 43556344 43574618 ENSG00000196793.13 ZNF239
chr8 144720907 144756417 ENSG00000198169.8 ZNF251
chr19 52797409 52857600 ENSG00000198538.10 ZNF28
chr17 18658429 18682262 ENSG00000249459.8 ZNF286B
chr19 34677639 34686397 ENSG00000089335.20 ZNF302
chr10 38094334 38150293 ENSG00000075407.18 ZNF37A
chr19 57900296 57916610 ENSG00000173480.10 ZNF417
chr19 57487711 57496097 ENSG00000105136.20 ZNF419
chr19 52031379 52095738 ENSG00000256087.6 ZNF432
chr19 19785839 19821751 ENSG00000081665.13 ZNF506
chr19 36534774 36605276 ENSG00000186020.12 ZNF529
chr19 7069444 7087968 ENSG00000130544.11 ZNF557
chr19 36182060 36246257 ENSG00000196357.11 ZNF565
chr17 5179536 5191883 ENSG00000180626.9 ZNF594
chr19 52012765 52030240 ENSG00000142556.18 ZNF614
chr19 21291160 21329425 ENSG00000182141.10 ZNF708
chr16 31713229 31794869 ENSG00000197302.10 ZNF720
chrX 135248920 135344087 ENSG00000186376.14 ZNF75D
chr19 53431993 53458261 ENSG00000160336.14 ZNF761
chr19 53389793 53430413 ENSG00000196417.12 ZNF765
chr19 52269571 52296046 ENSG00000196214.10 ZNF766
chr19 57466663 57477570 ENSG00000197128.11 ZNF772
chr19 57746796 57758159 ENSG00000152443.12 ZNF776
chr19 40028260 40056209 ENSG00000128000.15 ZNF780B
chrX 47836902 48002561 ENSG00000197779.13 ZNF81
chr19 57848731 57889074 ENSG00000204514.9 ZNF814
chr19 52949379 52962911 ENSG00000180257.13 ZNF816
chr19 52928475 52962823 ENSG00000221874.4 ZNF816-ZNF321P
chr19 11721265 11739009 ENSG00000197933.12 ZNF823
chr19 53333746 53356906 ENSG00000213799.12 ZNF845
chr3 44494847 44510636 ENSG00000178917.16 ZNF852
chr19 52904417 52923481 ENSG00000213793.5 ZNF888
chr2 135136916 135531236 ENSG00000121988.17 ZRANB3
chr18 35251058 35290245 ENSG00000186814.13 ZSCAN30
chr1 45016399 45306209 ENSG00000162415.6 ZSWIM5

LincRNAs overlaping peaks

Bear in mind that one peak can overlap ore than one genomic feature.

chrom start end gene_id gene_name
chr2 97416165 97433527 ENSG00000230606.10 AC092683.1
chr2 97421075 97434847 ENSG00000278766.2 AC092683.2
chr2 95807118 95816215 ENSG00000232931.5 LINC00342
chr22 30969245 30979395 ENSG00000253352.9 TUG1
chr22 30976515 30978848 ENSG00000269987.1 AC004542.2
chr22 30977516 30977858 ENSG00000269972.1 AC004542.1
chr2 97281904 97291780 ENSG00000277701.4 AC159540.2
chr6 71295173 71417436 ENSG00000269966.1 AL136164.2
chr6 71344344 71420769 ENSG00000233237.6 LINC00472
chr6 30234039 30326134 ENSG00000270604.5 HCG17
chr19 27684580 27793940 ENSG00000261824.6 LINC00662
chr19 27757184 27760849 ENSG00000261770.1 AC006504.1
chr13 95648733 95676925 ENSG00000247400.3 DNAJC3-DT
chr6 2245748 2482022 ENSG00000250903.8 GMDS-DT
chr11 59130133 59143015 ENSG00000245571.6 FAM111A-DT
chr19 19761038 19821716 ENSG00000267581.1 AC011477.4
chr18 3284145 3327292 ENSG00000266578.1 AP001025.1
chr5 43061395 43062441 ENSG00000272144.1 AC025171.4
chr8 142981738 143018437 ENSG00000247317.3 LY6E-DT
chr12 9240003 9257960 ENSG00000237248.5 LINC00987
chr12 9240406 9261050 ENSG00000256427.2 AC010175.1
chr1 148295895 148344636 ENSG00000224481.2 AC245100.1
chrX 115917271 115969089 ENSG00000235244.3 DANT2
chr21 22008944 22098459 ENSG00000233215.5 LINC01687
chr12 79341205 79503396 ENSG00000257894.2 AC027288.3
chr1 229258281 229271028 ENSG00000177788.5 AL162595.1
chr2 118132128 118222250 ENSG00000226856.6 THORLNC
chr10 125700436 125719566 ENSG00000224023.10 FLJ37035
chr14 28830244 28968400 ENSG00000258038.5 LINC02327
chr9 95759231 95875977 ENSG00000175611.11 LINC00476
chr21 15928296 16645065 ENSG00000215386.12 MIR99AHG
chr21 22098617 22116528 ENSG00000184856.6 LINC00308
chr6 140575788 140898381 ENSG00000285875.1 AL035446.2
chr19 53007512 53013180 ENSG00000267943.1 AC010328.1
chr4 134759399 134817289 ENSG00000249000.1 AC093722.1

Overlap with repeats

Families of repeats that overlap with peaks that are loss in TKO with respect to D3:

PieChart showing the proportion of classes of repeats overlapped by TKO/D3 peaks.

TKO/D3 peaks overlap with repetitive elements. Because H3K9me3 regions controlled by TASOR extend over many thousand of bases, most peaks overlap with more than one repeat. Their characteristics are summarised in Figure (pie chart).

This second piechart shows the same information but distributed into different bespoke categories.

## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] viridis_0.5.1        viridisLite_0.3.0    edgeR_3.26.8        
##  [4] limma_3.40.6         ggplot2_3.2.1        GenomicRanges_1.36.1
##  [7] GenomeInfoDb_1.20.0  IRanges_2.18.3       S4Vectors_0.22.1    
## [10] BiocGenerics_0.30.0  tidyr_1.0.0          kableExtra_1.1.0    
## [13] RColorBrewer_1.1-2   knitr_1.25          
## 
## loaded via a namespace (and not attached):
##  [1] locfit_1.5-9.1              Rcpp_1.0.2                 
##  [3] lattice_0.20-38             Rsamtools_2.0.2            
##  [5] Biostrings_2.52.0           assertthat_0.2.1           
##  [7] zeallot_0.1.0               digest_0.6.21              
##  [9] R6_2.4.0                    backports_1.1.5            
## [11] evaluate_0.14               highr_0.8                  
## [13] httr_1.4.1                  pillar_1.4.2               
## [15] zlibbioc_1.30.0             rlang_0.4.0                
## [17] lazyeval_0.2.2              rstudioapi_0.10            
## [19] Matrix_1.2-17               rmarkdown_1.16             
## [21] labeling_0.3                webshot_0.5.1              
## [23] BiocParallel_1.18.1         readr_1.3.1                
## [25] stringr_1.4.0               RCurl_1.95-4.12            
## [27] munsell_0.5.0               DelayedArray_0.10.0        
## [29] compiler_3.6.1              rtracklayer_1.44.4         
## [31] xfun_0.10                   pkgconfig_2.0.3            
## [33] htmltools_0.4.0             tidyselect_0.2.5           
## [35] SummarizedExperiment_1.14.1 gridExtra_2.3              
## [37] tibble_2.1.3                GenomeInfoDbData_1.2.1     
## [39] matrixStats_0.55.0          XML_3.98-1.20              
## [41] crayon_1.3.4                dplyr_0.8.3                
## [43] withr_2.1.2                 GenomicAlignments_1.20.1   
## [45] bitops_1.0-6                grid_3.6.1                 
## [47] gtable_0.3.0                lifecycle_0.1.0            
## [49] magrittr_1.5                scales_1.0.0               
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## [57] glue_1.3.1                  purrr_0.3.2                
## [59] hms_0.5.1                   yaml_2.2.0                 
## [61] colorspace_1.4-1            rvest_0.3.4