SCZ 2018 - Brain_Amygdala
sheng Qian
2021-2-6
Last updated: 2022-05-19
Checks: 5 2
Knit directory: cTWAS_analysis/
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library(reticulate)
use_python("/scratch/midway2/shengqian/miniconda3/envs/PythonForR/bin/python",required=T)Weight QC
#number of imputed weights
nrow(qclist_all)[1] 15774#number of imputed weights by chromosome
table(qclist_all$chr)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1480 1078 891 631 654 819 931 556 642 735 948 858 322 583 532 618
17 18 19 20 21 22
1087 198 1146 543 34 488 #number of imputed weights without missing variants
sum(qclist_all$nmiss==0)[1] 14087#proportion of imputed weights without missing variants
mean(qclist_all$nmiss==0)[1] 0.8931INFO:numexpr.utils:Note: NumExpr detected 56 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.finish
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionCheck convergence of parameters
| Version | Author | Date |
|---|---|---|
| 2749be9 | sq-96 | 2022-05-12 |
gene snp
0.0048321 0.0003214 gene snp
9.84 10.49 [1] 105318[1] 6393 6309950 gene snp
0.002886 0.202078 [1] 0.003939 1.090103Genes with highest PIPs
genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
6193 ZDHHC20 13_2 0.7353 24.63 1.277e-04 -4.784 3 4
1662 DPYSL3 5_86 0.7025 25.41 1.190e-04 -4.157 1 1
611 BDNF 11_19 0.6948 23.25 1.066e-04 -4.348 1 1
2984 LRP8 1_33 0.6357 24.92 1.347e-04 -4.820 3 3
3695 NTRK3 15_41 0.5946 22.72 7.628e-05 -4.457 1 1
2889 LINC00320 21_6 0.5011 28.32 1.382e-04 5.336 6 6
235 AKT3 1_128 0.4691 34.14 7.453e-05 6.266 5 5
2836 LAMA5 20_37 0.4676 30.04 9.116e-05 -4.371 10 14
561 B9D1 17_16 0.4377 28.72 5.225e-05 -5.282 1 1
897 CASP2 7_89 0.4319 22.43 3.974e-05 -3.889 1 1
4906 SF3B1 2_117 0.4313 43.83 7.836e-05 7.002 2 2
5966 UQCRC2 16_19 0.4042 22.91 3.555e-05 4.716 1 1
4828 SDCCAG8 1_128 0.3729 28.50 4.337e-05 5.612 5 8
1054 CECR2 22_2 0.3594 20.94 2.568e-05 3.928 1 1
552 B3GAT1 11_84 0.3480 25.37 4.977e-05 4.345 7 11
1554 DGKZ 11_28 0.3445 46.65 1.051e-04 7.216 2 2
510 ATP2B2 3_8 0.3195 31.83 4.405e-05 4.229 3 3
1605 DNAJB1 19_12 0.2911 19.50 1.569e-05 3.988 1 1
1482 DBF4B 17_26 0.2867 20.61 3.245e-05 -3.890 4 4
5487 TECR 19_12 0.2730 19.30 1.390e-05 3.972 3 3Genes with highest PVE
genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
2889 LINC00320 21_6 0.5011 28.32 1.382e-04 5.336 6 6
2984 LRP8 1_33 0.6357 24.92 1.347e-04 -4.820 3 3
6193 ZDHHC20 13_2 0.7353 24.63 1.277e-04 -4.784 3 4
1662 DPYSL3 5_86 0.7025 25.41 1.190e-04 -4.157 1 1
611 BDNF 11_19 0.6948 23.25 1.066e-04 -4.348 1 1
1554 DGKZ 11_28 0.3445 46.65 1.051e-04 7.216 2 2
2836 LAMA5 20_37 0.4676 30.04 9.116e-05 -4.371 10 14
4906 SF3B1 2_117 0.4313 43.83 7.836e-05 7.002 2 2
3695 NTRK3 15_41 0.5946 22.72 7.628e-05 -4.457 1 1
235 AKT3 1_128 0.4691 34.14 7.453e-05 6.266 5 5
371 APOPT1 14_54 0.2097 43.94 7.162e-05 -7.429 5 6
561 B9D1 17_16 0.4377 28.72 5.225e-05 -5.282 1 1
552 B3GAT1 11_84 0.3480 25.37 4.977e-05 4.345 7 11
370 APOM 6_26 0.2029 123.81 4.840e-05 11.541 2 2
510 ATP2B2 3_8 0.3195 31.83 4.405e-05 4.229 3 3
4828 SDCCAG8 1_128 0.3729 28.50 4.337e-05 5.612 5 8
897 CASP2 7_89 0.4319 22.43 3.974e-05 -3.889 1 1
5966 UQCRC2 16_19 0.4042 22.91 3.555e-05 4.716 1 1
2209 GIGYF2 2_137 0.2469 50.80 3.446e-05 -7.841 4 4
1482 DBF4B 17_26 0.2867 20.61 3.245e-05 -3.890 4 4Comparing z scores and PIPs
[1] 0.01611 genename region_tag susie_pip mu2 PVE z num_intron
3933 PGBD1 6_22 9.681e-03 157.22 1.473e-07 -13.087 2
370 APOM 6_26 2.029e-01 123.81 4.840e-05 11.541 2
1506 DDR1 6_26 1.524e-02 119.73 2.641e-07 -11.175 2
480 ATAT1 6_24 2.265e-02 79.41 3.868e-07 11.039 1
795 C6orf136 6_24 2.184e-02 79.12 7.164e-07 -11.031 2
2082 FLOT1 6_24 1.826e-02 77.80 1.418e-06 -10.981 6
568 BAG6 6_26 5.880e-04 108.10 3.549e-10 -10.247 4
4565 RNF5 6_26 6.016e-05 96.37 3.312e-12 -9.714 1
968 CCHCR1 6_26 7.875e-10 89.72 5.406e-22 -9.376 8
3686 NT5C2 10_66 1.533e-01 46.77 2.909e-05 -8.511 7
3043 MAD1L1 7_3 1.563e-01 63.35 1.665e-05 -8.215 3
2468 HLA-F 6_23 2.762e-02 61.03 4.672e-07 -8.066 2
2209 GIGYF2 2_137 2.469e-01 50.80 3.446e-05 -7.841 4
4685 RP5-874C20.8 6_22 5.863e-03 37.39 3.446e-08 7.631 4
6384 ZSCAN16 6_22 8.769e-03 52.88 5.447e-08 7.468 3
371 APOPT1 14_54 2.097e-01 43.94 7.162e-05 -7.429 5
1554 DGKZ 11_28 3.445e-01 46.65 1.051e-04 7.216 2
4968 SKIV2L 6_26 2.813e-08 77.27 5.804e-19 7.101 4
4906 SF3B1 2_117 4.313e-01 43.83 7.836e-05 7.002 2
485 ATG13 11_28 8.231e-02 43.02 5.534e-06 6.977 2
num_sqtl
3933 3
370 2
1506 2
480 1
795 2
2082 6
568 6
4565 1
968 12
3686 9
3043 3
2468 3
2209 4
4685 4
6384 3
371 6
1554 2
4968 5
4906 2
485 2GO enrichment analysis for genes with PIP>0.5
#number of genes for gene set enrichment
length(genes)[1] 6Uploading data to Enrichr... Done.
Querying GO_Biological_Process_2021... Done.
Querying GO_Cellular_Component_2021... Done.
Querying GO_Molecular_Function_2021... Done.
Parsing results... Done.
[1] "GO_Biological_Process_2021"
Term
1 positive regulation of neuron projection development (GO:0010976)
2 positive regulation of cell projection organization (GO:0031346)
3 regulation of neuron projection development (GO:0010975)
4 cellular response to nerve growth factor stimulus (GO:1990090)
5 regulation of trans-synaptic signaling (GO:0099177)
6 positive regulation of protein tyrosine kinase activity (GO:0061098)
7 positive regulation of phospholipase C activity (GO:0010863)
8 positive regulation of protein phosphorylation (GO:0001934)
9 positive regulation of peptidyl-serine phosphorylation (GO:0033138)
10 regulation of peptidyl-serine phosphorylation (GO:0033135)
11 modulation of chemical synaptic transmission (GO:0050804)
12 enzyme linked receptor protein signaling pathway (GO:0007167)
13 reelin-mediated signaling pathway (GO:0038026)
14 positive regulation of non-membrane spanning protein tyrosine kinase activity (GO:1903997)
15 positive regulation of receptor binding (GO:1900122)
16 regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)
17 regulation of non-membrane spanning protein tyrosine kinase activity (GO:1903995)
18 nucleobase catabolic process (GO:0046113)
19 positive regulation of signal transduction (GO:0009967)
20 pyrimidine nucleobase catabolic process (GO:0006208)
21 regulation of collateral sprouting (GO:0048670)
22 regulation of positive chemotaxis (GO:0050926)
23 regulation of receptor binding (GO:1900120)
24 nerve growth factor signaling pathway (GO:0038180)
25 positive regulation of dendritic spine morphogenesis (GO:0061003)
26 positive regulation of dendrite development (GO:1900006)
27 actin crosslink formation (GO:0051764)
28 pyrimidine nucleobase metabolic process (GO:0006206)
29 negative regulation of myotube differentiation (GO:0010832)
30 regulation of phospholipase C activity (GO:1900274)
31 neurotrophin TRK receptor signaling pathway (GO:0048011)
32 positive regulation of positive chemotaxis (GO:0050927)
33 pyrimidine-containing compound catabolic process (GO:0072529)
34 response to axon injury (GO:0048678)
35 positive regulation of CREB transcription factor activity (GO:0032793)
36 negative regulation of striated muscle cell differentiation (GO:0051154)
37 positive regulation of actin cytoskeleton reorganization (GO:2000251)
38 transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)
39 regulation of cell migration (GO:0030334)
40 positive regulation of dendrite morphogenesis (GO:0050775)
41 neurotrophin signaling pathway (GO:0038179)
42 positive regulation of dendritic spine development (GO:0060999)
43 peptidyl-L-cysteine S-palmitoylation (GO:0018230)
44 peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine (GO:0018231)
45 positive regulation of phospholipase activity (GO:0010518)
46 regulation of myotube differentiation (GO:0010830)
47 peripheral nervous system development (GO:0007422)
48 positive regulation of filopodium assembly (GO:0051491)
49 cellular response to cytokine stimulus (GO:0071345)
50 positive regulation of synapse assembly (GO:0051965)
51 regulation of response to biotic stimulus (GO:0002831)
52 protein palmitoylation (GO:0018345)
53 activation of protein kinase B activity (GO:0032148)
54 activation of phospholipase C activity (GO:0007202)
55 regulation of dendritic spine morphogenesis (GO:0061001)
56 actin filament bundle assembly (GO:0051017)
57 actin filament bundle organization (GO:0061572)
58 regulation of protein localization to cell surface (GO:2000008)
59 regulation of actin cytoskeleton reorganization (GO:2000249)
60 regulation of apoptotic signaling pathway (GO:2001233)
61 regulation of protein tyrosine kinase activity (GO:0061097)
62 protein acylation (GO:0043543)
63 regulation of dendrite development (GO:0050773)
64 regulation of filopodium assembly (GO:0051489)
65 positive regulation of axonogenesis (GO:0050772)
66 positive regulation of nervous system development (GO:0051962)
67 positive regulation of chemotaxis (GO:0050921)
68 regulation of cellular protein localization (GO:1903827)
69 regulation of synapse assembly (GO:0051963)
70 negative regulation of cell projection organization (GO:0031345)
71 positive regulation of developmental growth (GO:0048639)
72 plasma membrane bounded cell projection morphogenesis (GO:0120039)
73 positive regulation of cell junction assembly (GO:1901890)
74 positive regulation of protein binding (GO:0032092)
75 negative regulation of neuron projection development (GO:0010977)
76 protein lipidation (GO:0006497)
77 diterpenoid metabolic process (GO:0016101)
78 regulation of innate immune response (GO:0045088)
79 synapse assembly (GO:0007416)
80 establishment of protein localization to membrane (GO:0090150)
81 negative regulation of neuron apoptotic process (GO:0043524)
82 positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)
83 negative regulation of apoptotic signaling pathway (GO:2001234)
84 regulation of neuron differentiation (GO:0045664)
85 negative regulation of protein modification process (GO:0031400)
86 positive regulation of cytoskeleton organization (GO:0051495)
87 positive regulation of plasma membrane bounded cell projection assembly (GO:0120034)
88 regulation of defense response (GO:0031347)
89 negative regulation of phosphorylation (GO:0042326)
90 protein targeting to membrane (GO:0006612)
91 retinoid metabolic process (GO:0001523)
92 regulation of peptidyl-tyrosine phosphorylation (GO:0050730)
93 regulation of kinase activity (GO:0043549)
94 regulation of neuron apoptotic process (GO:0043523)
95 negative regulation of neuron death (GO:1901215)
96 positive regulation of cell growth (GO:0030307)
97 cell junction assembly (GO:0034329)
98 activation of GTPase activity (GO:0090630)
99 regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)
100 activation of protein kinase activity (GO:0032147)
101 negative regulation of cell motility (GO:2000146)
102 positive regulation of kinase activity (GO:0033674)
Overlap Adjusted.P.value Genes
1 4/88 7.870e-07 BDNF;NTRK3;DPYSL3;LRP8
2 3/117 2.909e-04 BDNF;NTRK3;DPYSL3
3 3/165 5.450e-04 BDNF;NTRK3;DPYSL3
4 2/22 6.523e-04 BDNF;NTRK3
5 2/35 1.342e-03 BDNF;LRP8
6 2/42 1.453e-03 BDNF;LRP8
7 2/43 1.453e-03 BDNF;NTRK3
8 3/371 2.293e-03 BDNF;NTRK3;LRP8
9 2/93 5.314e-03 BDNF;NTRK3
10 2/98 5.314e-03 BDNF;NTRK3
11 2/109 5.974e-03 BDNF;LRP8
12 2/140 9.015e-03 BDNF;NTRK3
13 1/5 1.646e-02 LRP8
14 1/6 1.646e-02 BDNF
15 1/6 1.646e-02 BDNF
16 1/7 1.646e-02 NTRK3
17 1/7 1.646e-02 BDNF
18 1/7 1.646e-02 DPYSL3
19 2/252 1.646e-02 BDNF;NTRK3
20 1/8 1.646e-02 DPYSL3
21 1/8 1.646e-02 BDNF
22 1/8 1.646e-02 NTRK3
23 1/10 1.810e-02 BDNF
24 1/10 1.810e-02 BDNF
25 1/10 1.810e-02 LRP8
26 1/11 1.914e-02 LRP8
27 1/12 1.939e-02 DPYSL3
28 1/12 1.939e-02 DPYSL3
29 1/13 2.028e-02 BDNF
30 1/15 2.188e-02 NTRK3
31 1/15 2.188e-02 BDNF
32 1/17 2.260e-02 NTRK3
33 1/17 2.260e-02 DPYSL3
34 1/18 2.260e-02 DPYSL3
35 1/18 2.260e-02 LRP8
36 1/19 2.260e-02 BDNF
37 1/19 2.260e-02 NTRK3
38 2/404 2.260e-02 BDNF;NTRK3
39 2/408 2.260e-02 NTRK3;DPYSL3
40 1/20 2.260e-02 LRP8
41 1/21 2.314e-02 BDNF
42 1/22 2.361e-02 LRP8
43 1/23 2.361e-02 ZDHHC20
44 1/23 2.361e-02 ZDHHC20
45 1/24 2.402e-02 NTRK3
46 1/25 2.402e-02 BDNF
47 1/25 2.402e-02 BDNF
48 1/26 2.446e-02 DPYSL3
49 2/482 2.512e-02 DPYSL3;LRP8
50 1/28 2.528e-02 BDNF
51 1/29 2.567e-02 LRP8
52 1/31 2.567e-02 ZDHHC20
53 1/31 2.567e-02 NTRK3
54 1/32 2.567e-02 BDNF
55 1/32 2.567e-02 LRP8
56 1/33 2.567e-02 DPYSL3
57 1/33 2.567e-02 DPYSL3
58 1/33 2.567e-02 BDNF
59 1/37 2.791e-02 NTRK3
60 1/38 2.791e-02 BDNF
61 1/39 2.791e-02 LRP8
62 1/39 2.791e-02 ZDHHC20
63 1/39 2.791e-02 LRP8
64 1/41 2.888e-02 DPYSL3
65 1/43 2.981e-02 BDNF
66 1/45 3.026e-02 BDNF
67 1/45 3.026e-02 NTRK3
68 1/46 3.047e-02 BDNF
69 1/47 3.068e-02 BDNF
70 1/49 3.152e-02 DPYSL3
71 1/52 3.251e-02 BDNF
72 1/52 3.251e-02 BDNF
73 1/57 3.478e-02 BDNF
74 1/58 3.478e-02 BDNF
75 1/58 3.478e-02 DPYSL3
76 1/61 3.609e-02 ZDHHC20
77 1/64 3.688e-02 LRP8
78 1/64 3.688e-02 LRP8
79 1/69 3.923e-02 BDNF
80 1/70 3.930e-02 ZDHHC20
81 1/71 3.936e-02 BDNF
82 1/77 4.214e-02 NTRK3
83 1/78 4.216e-02 BDNF
84 1/79 4.219e-02 BDNF
85 1/81 4.229e-02 NTRK3
86 1/82 4.229e-02 NTRK3
87 1/83 4.229e-02 DPYSL3
88 1/83 4.229e-02 LRP8
89 1/86 4.331e-02 NTRK3
90 1/87 4.332e-02 ZDHHC20
91 1/92 4.479e-02 LRP8
92 1/92 4.479e-02 LRP8
93 1/94 4.526e-02 NTRK3
94 1/98 4.617e-02 BDNF
95 1/98 4.617e-02 BDNF
96 1/102 4.704e-02 BDNF
97 1/102 4.704e-02 BDNF
98 1/105 4.787e-02 NTRK3
99 1/106 4.787e-02 NTRK3
100 1/114 4.992e-02 NTRK3
101 1/114 4.992e-02 DPYSL3
102 1/114 4.992e-02 NTRK3
[1] "GO_Cellular_Component_2021"
Term Overlap Adjusted.P.value
1 axon (GO:0030424) 2/204 0.01814
2 secretory vesicle (GO:0099503) 1/29 0.03063
3 exocytic vesicle (GO:0070382) 1/30 0.03063
4 neuron projection (GO:0043005) 2/556 0.03063
5 integral component of Golgi membrane (GO:0030173) 1/55 0.03063
6 caveola (GO:0005901) 1/60 0.03063
7 intrinsic component of Golgi membrane (GO:0031228) 1/60 0.03063
8 plasma membrane raft (GO:0044853) 1/82 0.03653
Genes
1 BDNF;NTRK3
2 DPYSL3
3 DPYSL3
4 BDNF;NTRK3
5 ZDHHC20
6 LRP8
7 ZDHHC20
8 LRP8
[1] "GO_Molecular_Function_2021"
Term
1 dihydropyrimidinase activity (GO:0004157)
2 neurotrophin binding (GO:0043121)
3 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)
4 filamin binding (GO:0031005)
5 death receptor binding (GO:0005123)
6 protein-cysteine S-palmitoyltransferase activity (GO:0019706)
7 palmitoyltransferase activity (GO:0016409)
8 transmembrane receptor protein tyrosine kinase activity (GO:0004714)
9 transmembrane receptor protein kinase activity (GO:0019199)
10 SH3 domain binding (GO:0017124)
11 acyltransferase activity, transferring groups other than amino-acyl groups (GO:0016747)
12 growth factor activity (GO:0008083)
13 protein tyrosine kinase activity (GO:0004713)
Overlap Adjusted.P.value Genes
1 1/6 0.01318 DPYSL3
2 1/8 0.01318 NTRK3
3 1/10 0.01318 DPYSL3
4 1/11 0.01318 DPYSL3
5 1/15 0.01437 BDNF
6 1/25 0.01982 ZDHHC20
7 1/29 0.01982 ZDHHC20
8 1/60 0.02953 NTRK3
9 1/60 0.02953 NTRK3
10 1/62 0.02953 DPYSL3
11 1/76 0.03285 ZDHHC20
12 1/87 0.03443 BDNF
13 1/108 0.03935 NTRK3DisGeNET enrichment analysis for genes with PIP>0.5
Description FDR Ratio BgRatio
51 Unipolar Depression 0.001280 3/3 259/9703
118 Major Depressive Disorder 0.001280 3/3 243/9703
47 Status Epilepticus 0.002185 2/3 68/9703
72 Petit mal status 0.002185 2/3 67/9703
79 Grand Mal Status Epilepticus 0.002185 2/3 67/9703
84 Complex Partial Status Epilepticus 0.002185 2/3 67/9703
113 Status Epilepticus, Subclinical 0.002185 2/3 67/9703
114 Non-Convulsive Status Epilepticus 0.002185 2/3 67/9703
115 Simple Partial Status Epilepticus 0.002185 2/3 67/9703
36 Nerve Degeneration 0.002935 2/3 83/9703WebGestalt enrichment analysis for genes with PIP>0.5
Warning: replacing previous import 'lifecycle::last_warnings' by
'rlang::last_warnings' when loading 'hms'Loading the functional categories...
Loading the ID list...
Loading the reference list...
Performing the enrichment analysis...Warning in oraEnrichment(interestGeneList, referenceGeneList, geneSet, minNum =
minNum, : No significant gene set is identified based on FDR 0.05!NULL
Sensitivity, specificity and precision for silver standard genes
#number of genes in known annotations
print(length(known_annotations))[1] 130#number of genes in known annotations with imputed expression
print(sum(known_annotations %in% ctwas_gene_res$genename))[1] 49#significance threshold for TWAS
print(sig_thresh)[1] 4.47#number of ctwas genes
length(ctwas_genes)[1] 0#number of TWAS genes
length(twas_genes)[1] 103#show novel genes (ctwas genes with not in TWAS genes)
ctwas_gene_res[ctwas_gene_res$genename %in% novel_genes,report_cols][1] genename region_tag susie_pip mu2 PVE z num_intron
[8] num_sqtl
<0 rows> (or 0-length row.names)#sensitivity / recall
print(sensitivity)ctwas TWAS
0.0 0.1 #specificity
print(specificity) ctwas TWAS
1.0000 0.9858 #precision / PPV
print(precision) ctwas TWAS
NaN 0.1262
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.4.0 forcats_0.5.1 stringr_1.4.0 purrr_0.3.4
[5] readr_1.4.0 tidyr_1.1.3 tidyverse_1.3.1 tibble_3.1.7
[9] WebGestaltR_0.4.4 disgenet2r_0.99.2 enrichR_3.0 cowplot_1.1.1
[13] ggplot2_3.3.5 dplyr_1.0.7 reticulate_1.25 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] fs_1.5.0 lubridate_1.7.10 doParallel_1.0.16 httr_1.4.2
[5] rprojroot_2.0.2 tools_4.1.0 backports_1.2.1 doRNG_1.8.2
[9] bslib_0.2.5.1 utf8_1.2.1 R6_2.5.0 vipor_0.4.5
[13] DBI_1.1.1 colorspace_2.0-2 withr_2.4.2 ggrastr_1.0.1
[17] tidyselect_1.1.1 processx_3.5.2 curl_4.3.2 compiler_4.1.0
[21] git2r_0.28.0 rvest_1.0.0 cli_3.0.0 Cairo_1.5-15
[25] xml2_1.3.2 labeling_0.4.2 sass_0.4.0 scales_1.1.1
[29] callr_3.7.0 systemfonts_1.0.4 apcluster_1.4.9 digest_0.6.27
[33] rmarkdown_2.9 svglite_2.0.0 pkgconfig_2.0.3 htmltools_0.5.1.1
[37] dbplyr_2.1.1 highr_0.9 rlang_1.0.2 rstudioapi_0.13
[41] jquerylib_0.1.4 farver_2.1.0 generics_0.1.0 jsonlite_1.7.2
[45] magrittr_2.0.1 Matrix_1.3-3 ggbeeswarm_0.6.0 Rcpp_1.0.7
[49] munsell_0.5.0 fansi_0.5.0 lifecycle_1.0.0 stringi_1.6.2
[53] whisker_0.4 yaml_2.2.1 plyr_1.8.6 grid_4.1.0
[57] ggrepel_0.9.1 parallel_4.1.0 promises_1.2.0.1 crayon_1.4.1
[61] lattice_0.20-44 haven_2.4.1 hms_1.1.0 knitr_1.33
[65] ps_1.6.0 pillar_1.7.0 igraph_1.2.6 rjson_0.2.20
[69] rngtools_1.5 reshape2_1.4.4 codetools_0.2-18 reprex_2.0.0
[73] glue_1.4.2 evaluate_0.14 getPass_0.2-2 modelr_0.1.8
[77] data.table_1.14.0 png_0.1-7 vctrs_0.3.8 httpuv_1.6.1
[81] foreach_1.5.1 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[85] xfun_0.24 broom_0.7.8 later_1.2.0 iterators_1.0.13
[89] beeswarm_0.4.0 ellipsis_0.3.2 here_1.0.1