Configuration Settings for the Workflow
species | tissue | metadata | genesets | genetype | min_umi_per_cell | max_mt_percent | min_genes_per_cell | min_cell | scr_th | seu_nrmlz_method | seu_scale_factor | seu_n_hvg | seu_n_dim | seu_k_param | seu_cluster_res | harmony | tsne | spr_n_dim | mrk_logfc | mrk_min_pct | mrk_only_pos | mrk_test | mrk_top_n | adt | trajectory | traj_var_gene | traj_top_n | pipe_version |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
hs | skin | sample_based | none | hgnc_symbol | 750 | 15 | 250 | 3 | 0.25 | LogNormalize | 1e+06 | 2000 | 30 | 20 | 0.7 | sample | FALSE | 30 | 0.25 | 0.5 | TRUE | wilcox | 0 | FALSE | none | 1000 | 50 | 1.0.0 |
sample | disease | skin_type | tissue | sample_id |
---|---|---|---|---|
NS-AR001 | Control | Nonlesion | Skin | S1 |
NS-AR003 | Control | Nonlesion | Skin | S2 |
NS-AR004 | Control | Nonlesion | Skin | S3 |
NS-AR005 | Control | Nonlesion | Skin | S4 |
NS-AR006 | Control | Nonlesion | Skin | S5 |
NS-AR007 | Control | Nonlesion | Skin | S6 |
NS-AR008 | Control | Nonlesion | Skin | S7 |
NS-AR009 | Control | Nonlesion | Skin | S8 |
PN-30696 | PSO | Nonlesion | Skin | S9 |
PN-30696V3 | PSO | Nonlesion | Skin | S10 |
PN-31170 | PSO | Nonlesion | Skin | S11 |
PN-31277 | PSO | Nonlesion | Skin | S12 |
PN-369PC | PSO | Nonlesion | Skin | S13 |
PN-5851 | PSO | Nonlesion | Skin | S14 |
PN-7802ED | PSO | Nonlesion | Skin | S15 |
PN-8659ED | PSO | Nonlesion | Skin | S16 |
PN-8940 | PSO | Nonlesion | Skin | S17 |
PN-929 | PSO | Nonlesion | Skin | S18 |
PN-9709PC | PSO | Nonlesion | Skin | S19 |
PP-30696 | PSO | Lesion | Skin | S20 |
PP-30696V3 | PSO | Lesion | Skin | S21 |
PP-31170 | PSO | Lesion | Skin | S22 |
PP-31277 | PSO | Lesion | Skin | S23 |
PP-31499 | PSO | Lesion | Skin | S24 |
PP-369PC | PSO | Lesion | Skin | S25 |
PP-5851 | PSO | Lesion | Skin | S26 |
PP-6215A | PSO | Lesion | Skin | S27 |
PP-6215B | PSO | Lesion | Skin | S28 |
PP-7802ED | PSO | Lesion | Skin | S29 |
PP-8659ED | PSO | Lesion | Skin | S30 |
PP-8940 | PSO | Lesion | Skin | S31 |
PP-929 | PSO | Lesion | Skin | S32 |
PP-9709PC | PSO | Lesion | Skin | S33 |
sample_id | pre_qc_gene | pre_qc_cell | post_qc_gene | post_qc_cell |
---|---|---|---|---|
S1 | 21,018 | 1,148 | 17,470 | 869 |
S2 | 21,473 | 2,345 | 18,157 | 2,032 |
S3 | 21,644 | 1,156 | 18,085 | 972 |
S4 | 20,585 | 1,064 | 17,121 | 901 |
S5 | 20,488 | 2,438 | 17,480 | 2,169 |
S6 | 21,940 | 2,880 | 18,873 | 2,650 |
S7 | 14,592 | 208 | 9,968 | 65 |
S8 | 20,805 | 2,295 | 17,635 | 2,085 |
S9 | 20,079 | 4,024 | 17,020 | 3,751 |
S10 | 19,855 | 1,563 | 16,370 | 1,207 |
S11 | 20,811 | 1,653 | 17,631 | 1,402 |
S12 | 21,293 | 3,522 | 18,057 | 3,255 |
S13 | 20,349 | 1,367 | 17,062 | 1,096 |
S14 | 20,335 | 3,386 | 16,909 | 2,879 |
S15 | 22,182 | 5,010 | 18,623 | 3,698 |
S16 | 22,409 | 3,273 | 19,152 | 2,471 |
S17 | 22,472 | 5,577 | 19,376 | 5,115 |
S18 | 19,969 | 5,216 | 16,927 | 4,717 |
S19 | 18,322 | 927 | 15,109 | 761 |
S20 | 21,067 | 3,339 | 17,834 | 2,788 |
S21 | 21,210 | 2,101 | 17,531 | 1,405 |
S22 | 22,475 | 3,746 | 19,488 | 3,168 |
S23 | 21,398 | 3,044 | 18,304 | 2,747 |
S24 | 21,801 | 2,843 | 18,757 | 2,395 |
S25 | 21,516 | 2,105 | 18,390 | 1,774 |
S26 | 20,472 | 1,153 | 16,873 | 809 |
S27 | 22,271 | 3,440 | 19,164 | 3,212 |
S28 | 22,627 | 4,077 | 19,497 | 3,808 |
S29 | 22,925 | 5,982 | 19,526 | 4,600 |
S30 | 22,668 | 3,177 | 19,414 | 2,687 |
S31 | 22,288 | 3,929 | 19,207 | 3,390 |
S32 | 21,478 | 5,106 | 18,435 | 4,315 |
S33 | 20,574 | 2,994 | 17,473 | 2,778 |
Vales are post-QC.
sample_id | min | 0% | 25% | 50% | 75% | 100% | max |
---|---|---|---|---|---|---|---|
S1 | 759 | 759 | 6,000 | 8,183 | 10,665 | 54,022 | 54,022 |
S2 | 751 | 751 | 8,481 | 13,656 | 19,624 | 54,609 | 54,609 |
S3 | 752 | 752 | 4,681 | 7,584 | 11,065 | 207,862 | 207,862 |
S4 | 751 | 751 | 4,645 | 7,713 | 16,742 | 261,100 | 261,100 |
S5 | 751 | 751 | 6,517 | 10,442 | 16,483 | 188,158 | 188,158 |
S6 | 770 | 770 | 7,502 | 13,544 | 17,142 | 82,763 | 82,763 |
S7 | 795 | 795 | 3,566 | 5,498 | 7,596 | 41,285 | 41,285 |
S8 | 752 | 752 | 5,885 | 9,198 | 11,358 | 47,767 | 47,767 |
S9 | 750 | 750 | 4,447 | 6,168 | 8,280 | 28,999 | 28,999 |
S10 | 752 | 752 | 9,012 | 12,346 | 17,034 | 62,224 | 62,224 |
S11 | 751 | 751 | 2,872 | 5,335 | 8,798 | 75,021 | 75,021 |
S12 | 751 | 751 | 2,934 | 6,930 | 10,844 | 72,570 | 72,570 |
S13 | 758 | 758 | 3,990 | 7,296 | 12,308 | 54,000 | 54,000 |
S14 | 752 | 752 | 5,573 | 7,361 | 9,671 | 56,430 | 56,430 |
S15 | 756 | 756 | 2,910 | 6,076 | 8,774 | 48,617 | 48,617 |
S16 | 750 | 750 | 4,084 | 6,993 | 11,302 | 119,244 | 119,244 |
S17 | 750 | 750 | 4,198 | 8,481 | 12,540 | 51,723 | 51,723 |
S18 | 778 | 778 | 6,426 | 9,036 | 11,851 | 51,642 | 51,642 |
S19 | 751 | 751 | 6,712 | 11,750 | 15,767 | 61,526 | 61,526 |
S20 | 751 | 751 | 3,188 | 7,261 | 12,164 | 94,706 | 94,706 |
S21 | 750 | 750 | 3,128 | 6,951 | 17,405 | 84,908 | 84,908 |
S22 | 750 | 750 | 4,148 | 9,386 | 19,072 | 93,007 | 93,007 |
S23 | 750 | 750 | 5,688 | 13,683 | 21,342 | 90,463 | 90,463 |
S24 | 770 | 770 | 5,530 | 16,064 | 26,234 | 91,984 | 91,984 |
S25 | 750 | 750 | 7,173 | 15,594 | 25,385 | 105,019 | 105,019 |
S26 | 750 | 750 | 8,693 | 16,253 | 25,801 | 126,353 | 126,353 |
S27 | 760 | 760 | 4,066 | 10,548 | 20,321 | 112,201 | 112,201 |
S28 | 755 | 755 | 4,210 | 10,302 | 19,992 | 120,547 | 120,547 |
S29 | 753 | 753 | 5,269 | 9,740 | 16,104 | 57,299 | 57,299 |
S30 | 759 | 759 | 3,881 | 6,788 | 11,608 | 78,449 | 78,449 |
S31 | 750 | 750 | 2,899 | 5,770 | 12,609 | 112,431 | 112,431 |
S32 | 772 | 772 | 8,142 | 11,714 | 16,932 | 68,083 | 68,083 |
S33 | 755 | 755 | 3,096 | 7,483 | 9,936 | 38,875 | 38,875 |
Vales are post-QC.
sample_id | min | 0% | 25% | 50% | 75% | 100% | max |
---|---|---|---|---|---|---|---|
S1 | 369 | 369 | 1,986 | 2,725 | 3,243 | 6,293 | 6,293 |
S2 | 338 | 338 | 2,268 | 2,912 | 3,604 | 7,156 | 7,156 |
S3 | 334 | 334 | 1,704 | 2,646 | 3,362 | 9,038 | 9,038 |
S4 | 330 | 330 | 1,783 | 2,465 | 3,360 | 9,378 | 9,378 |
S5 | 314 | 314 | 2,026 | 2,624 | 3,442 | 9,582 | 9,582 |
S6 | 267 | 267 | 2,502 | 3,348 | 3,874 | 7,948 | 7,948 |
S7 | 355 | 355 | 1,109 | 1,893 | 2,479 | 5,808 | 5,808 |
S8 | 413 | 413 | 2,032 | 2,547 | 2,971 | 6,150 | 6,150 |
S9 | 300 | 300 | 1,358 | 1,654 | 1,996 | 4,411 | 4,411 |
S10 | 342 | 342 | 2,422 | 2,947 | 3,475 | 7,880 | 7,880 |
S11 | 266 | 266 | 1,215 | 1,884 | 2,602 | 7,822 | 7,822 |
S12 | 283 | 283 | 1,134 | 1,770 | 2,312 | 5,979 | 5,979 |
S13 | 344 | 344 | 1,554 | 2,170 | 2,780 | 7,558 | 7,558 |
S14 | 366 | 366 | 1,627 | 1,981 | 2,424 | 6,536 | 6,536 |
S15 | 275 | 275 | 1,187 | 1,966 | 2,434 | 5,802 | 5,802 |
S16 | 322 | 322 | 1,562 | 2,308 | 3,096 | 8,702 | 8,702 |
S17 | 317 | 317 | 1,618 | 2,275 | 2,797 | 6,161 | 6,161 |
S18 | 421 | 421 | 1,647 | 2,027 | 2,433 | 5,194 | 5,194 |
S19 | 328 | 328 | 1,869 | 2,386 | 2,790 | 6,017 | 6,017 |
S20 | 293 | 293 | 1,223 | 2,100 | 2,734 | 6,685 | 6,685 |
S21 | 379 | 379 | 1,361 | 2,342 | 3,571 | 7,784 | 7,784 |
S22 | 268 | 268 | 1,521 | 2,632 | 3,566 | 7,939 | 7,939 |
S23 | 287 | 287 | 1,708 | 2,736 | 3,442 | 7,309 | 7,309 |
S24 | 296 | 296 | 1,924 | 3,354 | 4,130 | 6,912 | 6,912 |
S25 | 294 | 294 | 2,165 | 3,399 | 4,260 | 7,179 | 7,179 |
S26 | 334 | 334 | 2,707 | 3,775 | 4,692 | 8,842 | 8,842 |
S27 | 374 | 374 | 1,544 | 2,824 | 3,879 | 7,196 | 7,196 |
S28 | 300 | 300 | 1,619 | 2,788 | 3,838 | 7,376 | 7,376 |
S29 | 303 | 303 | 1,826 | 2,670 | 3,369 | 5,699 | 5,699 |
S30 | 350 | 350 | 1,528 | 2,287 | 3,123 | 8,279 | 8,279 |
S31 | 256 | 256 | 1,254 | 1,936 | 3,012 | 7,959 | 7,959 |
S32 | 278 | 278 | 2,192 | 2,711 | 3,346 | 5,974 | 5,974 |
S33 | 345 | 345 | 1,247 | 1,922 | 2,333 | 4,951 | 4,951 |
Vales are post-QC.
sample_id | min | 0% | 25% | 50% | 75% | 100% | max |
---|---|---|---|---|---|---|---|
S1 | 0.00 | 0.00 | 4.29 | 6.19 | 8.39 | 14.93 | 14.93 |
S2 | 0.00 | 0.00 | 2.41 | 3.23 | 4.41 | 14.85 | 14.85 |
S3 | 0.00 | 0.00 | 2.43 | 3.92 | 5.60 | 14.89 | 14.89 |
S4 | 0.00 | 0.00 | 0.48 | 1.44 | 3.47 | 14.97 | 14.97 |
S5 | 0.05 | 0.05 | 2.13 | 2.96 | 4.28 | 14.62 | 14.62 |
S6 | 0.00 | 0.00 | 1.27 | 3.47 | 5.07 | 14.77 | 14.77 |
S7 | 1.23 | 1.23 | 3.58 | 4.70 | 6.34 | 13.96 | 13.96 |
S8 | 0.00 | 0.00 | 0.55 | 1.42 | 2.95 | 14.95 | 14.95 |
S9 | 0.00 | 0.00 | 1.84 | 2.38 | 3.17 | 14.76 | 14.76 |
S10 | 0.00 | 0.00 | 4.53 | 5.96 | 7.59 | 14.99 | 14.99 |
S11 | 0.02 | 0.02 | 2.05 | 2.94 | 4.05 | 14.93 | 14.93 |
S12 | 0.00 | 0.00 | 1.59 | 2.10 | 2.85 | 13.62 | 13.62 |
S13 | 0.03 | 0.03 | 0.85 | 1.53 | 2.79 | 14.80 | 14.80 |
S14 | 0.00 | 0.00 | 6.42 | 7.98 | 9.67 | 14.96 | 14.96 |
S15 | 0.08 | 0.08 | 3.78 | 5.09 | 6.90 | 15.00 | 15.00 |
S16 | 0.23 | 0.23 | 4.92 | 6.61 | 8.81 | 14.99 | 14.99 |
S17 | 0.05 | 0.05 | 2.94 | 3.63 | 4.42 | 14.80 | 14.80 |
S18 | 0.00 | 0.00 | 2.79 | 3.57 | 4.57 | 14.64 | 14.64 |
S19 | 0.00 | 0.00 | 2.87 | 3.62 | 4.56 | 14.68 | 14.68 |
S20 | 0.00 | 0.00 | 2.18 | 3.09 | 4.47 | 14.94 | 14.94 |
S21 | 0.00 | 0.00 | 5.35 | 7.37 | 9.89 | 14.99 | 14.99 |
S22 | 0.00 | 0.00 | 1.73 | 2.81 | 3.99 | 14.88 | 14.88 |
S23 | 0.00 | 0.00 | 1.43 | 2.04 | 2.68 | 14.90 | 14.90 |
S24 | 0.00 | 0.00 | 1.59 | 2.04 | 2.71 | 14.99 | 14.99 |
S25 | 0.00 | 0.00 | 2.22 | 2.99 | 3.73 | 14.80 | 14.80 |
S26 | 0.00 | 0.00 | 2.24 | 4.91 | 7.72 | 14.97 | 14.97 |
S27 | 0.00 | 0.00 | 2.22 | 2.94 | 3.75 | 14.84 | 14.84 |
S28 | 0.00 | 0.00 | 2.16 | 2.86 | 3.66 | 14.96 | 14.96 |
S29 | 0.00 | 0.00 | 4.60 | 6.08 | 7.57 | 14.99 | 14.99 |
S30 | 0.06 | 0.06 | 4.38 | 5.84 | 7.70 | 14.99 | 14.99 |
S31 | 0.02 | 0.02 | 2.46 | 3.37 | 4.55 | 14.99 | 14.99 |
S32 | 0.00 | 0.00 | 3.53 | 4.33 | 5.53 | 14.99 | 14.99 |
S33 | 0.00 | 0.00 | 0.73 | 1.42 | 2.03 | 14.46 | 14.46 |
Thresholds, represented by dashed lines, were implemented to filter the data and only retain cells of high quality.
Number of barcodes shared between pairs of samples post-QC.
S1 | S2 | S3 | S4 | S5 | S6 | S7 | S8 | S9 | S10 | S11 | S12 | S13 | S14 | S15 | S16 | S17 | S18 | S19 | S20 | S21 | S22 | S23 | S24 | S25 | S26 | S27 | S28 | S29 | S30 | S31 | S32 | S33 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
S1 | 869 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 |
S2 | 0 | 2032 | 3 | 2 | 1 | 0 | 0 | 0 | 0 | 2 | 0 | 1 | 0 | 2 | 1 | 3 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
S3 | 0 | 3 | 972 | 3 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 1 |
S4 | 0 | 2 | 3 | 901 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
S5 | 0 | 1 | 0 | 1 | 2169 | 3 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 5 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 3 | 0 | 0 | 0 |
S6 | 0 | 0 | 0 | 0 | 3 | 2650 | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 2 | 3 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 2 | 0 | 0 | 0 |
S7 | 0 | 0 | 0 | 0 | 0 | 0 | 65 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
S8 | 0 | 0 | 1 | 0 | 2 | 2 | 1 | 2085 | 0 | 1 | 0 | 0 | 0 | 2 | 0 | 1 | 0 | 2 | 0 | 0 | 3 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 3 | 2 | 0 | 0 | 0 |
S9 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3751 | 0 | 1 | 18 | 6 | 0 | 0 | 0 | 30 | 22 | 2 | 16 | 0 | 17 | 14 | 13 | 6 | 0 | 20 | 20 | 1 | 1 | 16 | 25 | 20 |
S10 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1207 | 0 | 1 | 0 | 3 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 2 | 0 | 0 | 0 |
S11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1402 | 6 | 0 | 0 | 0 | 1 | 4 | 11 | 2 | 6 | 0 | 30 | 8 | 3 | 4 | 0 | 4 | 6 | 0 | 1 | 4 | 7 | 3 |
S12 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 18 | 1 | 6 | 3255 | 6 | 0 | 1 | 0 | 17 | 29 | 2 | 18 | 0 | 9 | 13 | 9 | 4 | 0 | 15 | 12 | 0 | 0 | 15 | 13 | 17 |
S13 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 6 | 0 | 0 | 6 | 1096 | 0 | 0 | 0 | 8 | 11 | 1 | 5 | 1 | 5 | 3 | 3 | 15 | 0 | 0 | 4 | 0 | 0 | 4 | 8 | 4 |
S14 | 0 | 2 | 1 | 0 | 5 | 2 | 1 | 2 | 0 | 3 | 0 | 0 | 0 | 2879 | 1 | 2 | 0 | 0 | 0 | 2 | 2 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 6 | 4 | 0 | 0 | 1 |
S15 | 3 | 1 | 1 | 2 | 2 | 3 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 3698 | 2 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 3 | 3 | 0 | 0 | 0 |
S16 | 0 | 3 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 1 | 1 | 0 | 0 | 2 | 2 | 2471 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 4 | 0 | 0 | 0 |
S17 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 30 | 1 | 4 | 17 | 8 | 0 | 0 | 0 | 5115 | 35 | 8 | 18 | 0 | 28 | 24 | 10 | 12 | 0 | 18 | 32 | 0 | 1 | 21 | 36 | 19 |
S18 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 22 | 0 | 11 | 29 | 11 | 0 | 0 | 0 | 35 | 4717 | 4 | 16 | 0 | 17 | 24 | 21 | 10 | 0 | 22 | 25 | 0 | 1 | 25 | 23 | 15 |
S19 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 2 | 2 | 1 | 0 | 0 | 0 | 8 | 4 | 761 | 7 | 0 | 1 | 9 | 5 | 3 | 0 | 2 | 3 | 0 | 0 | 1 | 3 | 14 |
S20 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 16 | 0 | 6 | 18 | 5 | 2 | 0 | 0 | 18 | 16 | 7 | 2788 | 0 | 13 | 8 | 7 | 2 | 0 | 15 | 13 | 0 | 0 | 13 | 12 | 9 |
S21 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 1 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 1405 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 0 |
S22 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 17 | 0 | 30 | 9 | 5 | 0 | 1 | 1 | 28 | 17 | 1 | 13 | 0 | 3168 | 18 | 17 | 5 | 0 | 15 | 14 | 0 | 0 | 14 | 18 | 8 |
S23 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 14 | 0 | 8 | 13 | 3 | 1 | 0 | 0 | 24 | 24 | 9 | 8 | 0 | 18 | 2747 | 9 | 5 | 0 | 10 | 17 | 0 | 1 | 11 | 14 | 8 |
S24 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 13 | 0 | 3 | 9 | 3 | 0 | 0 | 0 | 10 | 21 | 5 | 7 | 0 | 17 | 9 | 2395 | 4 | 0 | 9 | 11 | 0 | 0 | 10 | 10 | 6 |
S25 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 6 | 0 | 4 | 4 | 15 | 0 | 1 | 0 | 12 | 10 | 3 | 2 | 0 | 5 | 5 | 4 | 1774 | 0 | 4 | 12 | 0 | 0 | 9 | 15 | 2 |
S26 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 809 | 0 | 0 | 1 | 1 | 0 | 0 | 0 |
S27 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 20 | 0 | 4 | 15 | 0 | 0 | 0 | 0 | 18 | 22 | 2 | 15 | 0 | 15 | 10 | 9 | 4 | 0 | 3212 | 12 | 1 | 0 | 15 | 23 | 13 |
S28 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 20 | 0 | 6 | 12 | 4 | 1 | 1 | 0 | 32 | 25 | 3 | 13 | 0 | 14 | 17 | 11 | 12 | 0 | 12 | 3808 | 1 | 0 | 23 | 25 | 16 |
S29 | 2 | 1 | 2 | 1 | 4 | 1 | 0 | 3 | 1 | 1 | 0 | 0 | 0 | 6 | 3 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 4600 | 3 | 0 | 0 | 0 |
S30 | 1 | 1 | 0 | 0 | 3 | 2 | 0 | 2 | 1 | 2 | 1 | 0 | 0 | 4 | 3 | 4 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 3 | 2687 | 1 | 0 | 0 |
S31 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 16 | 0 | 4 | 15 | 4 | 0 | 0 | 0 | 21 | 25 | 1 | 13 | 0 | 14 | 11 | 10 | 9 | 0 | 15 | 23 | 0 | 1 | 3390 | 17 | 11 |
S32 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 25 | 0 | 7 | 13 | 8 | 0 | 0 | 0 | 36 | 23 | 3 | 12 | 1 | 18 | 14 | 10 | 15 | 0 | 23 | 25 | 0 | 0 | 17 | 4315 | 17 |
S33 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 20 | 0 | 3 | 17 | 4 | 1 | 0 | 0 | 19 | 15 | 14 | 9 | 0 | 8 | 8 | 6 | 2 | 0 | 13 | 16 | 0 | 0 | 11 | 17 | 2778 |
Fraction (%) of barcodes shared between pairs of samples post-QC.
S1 | S2 | S3 | S4 | S5 | S6 | S7 | S8 | S9 | S10 | S11 | S12 | S13 | S14 | S15 | S16 | S17 | S18 | S19 | S20 | S21 | S22 | S23 | S24 | S25 | S26 | S27 | S28 | S29 | S30 | S31 | S32 | S33 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
S1 | 100.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 |
S2 | 0.00 | 100.00 | 0.20 | 0.14 | 0.05 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.04 | 0.00 | 0.08 | 0.03 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0e+00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.00 | 0.00 |
S3 | 0.00 | 0.20 | 100.00 | 0.32 | 0.00 | 0.00 | 0e+00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.05 |
S4 | 0.00 | 0.14 | 0.32 | 100.00 | 0.07 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 |
S5 | 0.00 | 0.05 | 0.00 | 0.07 | 100.00 | 0.12 | 0e+00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.20 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.12 | 0.12 | 0.00 | 0.00 | 0.00 |
S6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 100.00 | 0e+00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 6e-02 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 |
S7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1e+02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
S8 | 0.00 | 0.00 | 0.07 | 0.00 | 0.09 | 0.08 | 9e-02 | 100.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.04 | 0.00 | 0.06 | 0.00 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.10 | 0e+00 | 0.00 | 0.00 | 0.09 | 0.08 | 0.00 | 0.00 | 0.00 |
S9 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 100.00 | 0.00 | 0.04 | 0.51 | 0.25 | 0.00 | 0.00 | 0.00 | 0.68 | 0.52 | 0.09 | 0.49 | 0.00 | 0.49 | 0.43 | 0.42 | 0.22 | 0e+00 | 0.57 | 0.53 | 0.02 | 0.03 | 0.45 | 0.62 | 0.61 |
S10 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.06 | 0.00 | 100.00 | 0.00 | 0.04 | 0.00 | 0.15 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 |
S11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.04 | 0.00 | 100.00 | 0.26 | 0.00 | 0.00 | 0.00 | 0.05 | 0.12 | 0.36 | 0.18 | 0.29 | 0.00 | 1.31 | 0.39 | 0.16 | 0.25 | 0e+00 | 0.17 | 0.23 | 0.00 | 0.05 | 0.17 | 0.24 | 0.14 |
S12 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.51 | 0.04 | 0.26 | 100.00 | 0.28 | 0.00 | 0.03 | 0.00 | 0.41 | 0.73 | 0.10 | 0.60 | 0.00 | 0.28 | 0.43 | 0.32 | 0.16 | 0e+00 | 0.46 | 0.34 | 0.00 | 0.00 | 0.45 | 0.34 | 0.56 |
S13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0e+00 | 0.00 | 0.25 | 0.00 | 0.00 | 0.28 | 100.00 | 0.00 | 0.00 | 0.00 | 0.26 | 0.38 | 0.11 | 0.26 | 0.08 | 0.23 | 0.16 | 0.17 | 1.05 | 0e+00 | 0.00 | 0.16 | 0.00 | 0.00 | 0.18 | 0.30 | 0.21 |
S14 | 0.00 | 0.08 | 0.05 | 0.00 | 0.20 | 0.07 | 7e-02 | 0.08 | 0.00 | 0.15 | 0.00 | 0.00 | 0.00 | 100.00 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.07 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.03 | 0.16 | 0.14 | 0.00 | 0.00 | 0.04 |
S15 | 0.13 | 0.03 | 0.04 | 0.09 | 0.07 | 0.09 | 0e+00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 100.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.04 | 0e+00 | 0.00 | 0.03 | 0.07 | 0.09 | 0.00 | 0.00 | 0.00 |
S16 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.00 | 8e-02 | 0.04 | 0.00 | 0.05 | 0.05 | 0.00 | 0.00 | 0.07 | 0.06 | 100.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.00 | 0.03 | 0.16 | 0.00 | 0.00 | 0.00 |
S17 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.68 | 0.03 | 0.12 | 0.41 | 0.26 | 0.00 | 0.00 | 0.00 | 100.00 | 0.71 | 0.27 | 0.46 | 0.00 | 0.68 | 0.61 | 0.27 | 0.35 | 0e+00 | 0.43 | 0.72 | 0.00 | 0.03 | 0.49 | 0.76 | 0.48 |
S18 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.06 | 0.52 | 0.00 | 0.36 | 0.73 | 0.38 | 0.00 | 0.00 | 0.00 | 0.71 | 100.00 | 0.15 | 0.43 | 0.00 | 0.43 | 0.64 | 0.59 | 0.31 | 0e+00 | 0.55 | 0.59 | 0.00 | 0.03 | 0.62 | 0.51 | 0.40 |
S19 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.09 | 0.00 | 0.18 | 0.10 | 0.11 | 0.00 | 0.00 | 0.00 | 0.27 | 0.15 | 100.00 | 0.39 | 0.00 | 0.05 | 0.51 | 0.32 | 0.24 | 0e+00 | 0.10 | 0.13 | 0.00 | 0.00 | 0.05 | 0.12 | 0.79 |
S20 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0e+00 | 0.00 | 0.49 | 0.00 | 0.29 | 0.60 | 0.26 | 0.07 | 0.00 | 0.00 | 0.46 | 0.43 | 0.39 | 100.00 | 0.00 | 0.44 | 0.29 | 0.27 | 0.09 | 0e+00 | 0.50 | 0.39 | 0.00 | 0.00 | 0.42 | 0.34 | 0.32 |
S21 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 | 0.00 | 9e-02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 |
S22 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0e+00 | 0.00 | 0.49 | 0.00 | 1.31 | 0.28 | 0.23 | 0.00 | 0.03 | 0.04 | 0.68 | 0.43 | 0.05 | 0.44 | 0.00 | 100.00 | 0.61 | 0.61 | 0.20 | 0e+00 | 0.47 | 0.40 | 0.00 | 0.00 | 0.43 | 0.48 | 0.27 |
S23 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.43 | 0.00 | 0.39 | 0.43 | 0.16 | 0.04 | 0.00 | 0.00 | 0.61 | 0.64 | 0.51 | 0.29 | 0.00 | 0.61 | 100.00 | 0.35 | 0.22 | 0e+00 | 0.34 | 0.52 | 0.00 | 0.04 | 0.36 | 0.40 | 0.29 |
S24 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.42 | 0.00 | 0.16 | 0.32 | 0.17 | 0.00 | 0.00 | 0.00 | 0.27 | 0.59 | 0.32 | 0.27 | 0.00 | 0.61 | 0.35 | 100.00 | 0.19 | 0e+00 | 0.32 | 0.35 | 0.00 | 0.00 | 0.35 | 0.30 | 0.23 |
S25 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.10 | 0.22 | 0.00 | 0.25 | 0.16 | 1.05 | 0.00 | 0.04 | 0.00 | 0.35 | 0.31 | 0.24 | 0.09 | 0.00 | 0.20 | 0.22 | 0.19 | 100.00 | 0e+00 | 0.16 | 0.43 | 0.00 | 0.00 | 0.35 | 0.49 | 0.09 |
S26 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0e+00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 1e+02 | 0.00 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 |
S27 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.57 | 0.00 | 0.17 | 0.46 | 0.00 | 0.00 | 0.00 | 0.00 | 0.43 | 0.55 | 0.10 | 0.50 | 0.00 | 0.47 | 0.34 | 0.32 | 0.16 | 0e+00 | 100.00 | 0.34 | 0.03 | 0.00 | 0.45 | 0.61 | 0.43 |
S28 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0e+00 | 0.00 | 0.53 | 0.00 | 0.23 | 0.34 | 0.16 | 0.03 | 0.03 | 0.00 | 0.72 | 0.59 | 0.13 | 0.39 | 0.00 | 0.40 | 0.52 | 0.35 | 0.43 | 0e+00 | 0.34 | 100.00 | 0.02 | 0.00 | 0.64 | 0.62 | 0.49 |
S29 | 0.07 | 0.03 | 0.07 | 0.04 | 0.12 | 0.03 | 0e+00 | 0.09 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.16 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 4e-02 | 0.03 | 0.02 | 100.00 | 0.08 | 0.00 | 0.00 | 0.00 |
S30 | 0.06 | 0.04 | 0.00 | 0.00 | 0.12 | 0.07 | 0e+00 | 0.08 | 0.03 | 0.10 | 0.05 | 0.00 | 0.00 | 0.14 | 0.09 | 0.16 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 6e-02 | 0.00 | 0.00 | 0.08 | 100.00 | 0.03 | 0.00 | 0.00 |
S31 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.45 | 0.00 | 0.17 | 0.45 | 0.18 | 0.00 | 0.00 | 0.00 | 0.49 | 0.62 | 0.05 | 0.42 | 0.00 | 0.43 | 0.36 | 0.35 | 0.35 | 0e+00 | 0.45 | 0.64 | 0.00 | 0.03 | 100.00 | 0.44 | 0.36 |
S32 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.62 | 0.00 | 0.24 | 0.34 | 0.30 | 0.00 | 0.00 | 0.00 | 0.76 | 0.51 | 0.12 | 0.34 | 0.03 | 0.48 | 0.40 | 0.30 | 0.49 | 0e+00 | 0.61 | 0.62 | 0.00 | 0.00 | 0.44 | 100.00 | 0.48 |
S33 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0e+00 | 0.00 | 0.61 | 0.00 | 0.14 | 0.56 | 0.21 | 0.04 | 0.00 | 0.00 | 0.48 | 0.40 | 0.79 | 0.32 | 0.00 | 0.27 | 0.29 | 0.23 | 0.09 | 0e+00 | 0.43 | 0.49 | 0.00 | 0.00 | 0.36 | 0.48 | 100.00 |
Observed scores are used for doublet classification. Dashed line indicates the threshold used to identify doublets.
diamonds and diamonds refer to before and after QC, respectively.
The error bars represent the standard deviation of the number of UMIs and genes across cells per sample.
min | 0% | 25% | 50% | 75% | 100% | max | |
---|---|---|---|---|---|---|---|
UMI per cell | 750 | 750 | 4,608 | 8,679 | 14,068 | 261,100 | 261,100 |
Gene per cell | 256 | 256 | 1,583 | 2,316 | 3,140 | 9,582 | 9,582 |
Mitochondrial (%) per cell | 0.00 | 0.00 | 2.18 | 3.44 | 5.32 | 15.00 | 15.00 |
Note: Labels may have been removed if they overlap excessively.
Note: QC metrics based on kernel density estimation.
Note: Labels may have been removed if they overlap excessively.
Values at the top of each bar indicate the percentage of cells
This measurement is a proxy to batch effect artifacts. Values adjacent to each point indicate the number of cells.
Note: Labels may have been removed if they overlap excessively.
Values at the top of each bar indicate the percentage of cells
Publication: no referrence
Data Availability: no referrence
This is the output of sessionInfo()
on the computing
system on which this document was compiled
## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## Random number generation:
## RNG: L'Ecuyer-CMRG
## Normal: Inversion
## Sample: Rejection
##
## locale:
## [1] C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 grid stats graphics grDevices
## [6] utils datasets methods base
##
## other attached packages:
## [1] edgeR_4.0.2 limma_3.58.1
## [3] slingshot_2.10.0 TrajectoryUtils_1.10.0
## [5] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
## [7] Biobase_2.62.0 GenomicRanges_1.54.1
## [9] GenomeInfoDb_1.38.1 IRanges_2.36.0
## [11] S4Vectors_0.40.2 BiocGenerics_0.48.1
## [13] MatrixGenerics_1.14.0 matrixStats_1.1.0
## [15] princurve_2.1.6 Nebulosa_1.12.0
## [17] patchwork_1.1.3 data.table_1.14.10
## [19] ComplexHeatmap_2.18.0 visNetwork_2.1.2
## [21] plotly_4.10.3 data.tree_1.1.0
## [23] DT_0.30 readxl_1.4.3
## [25] gtools_3.9.5 gplots_3.1.3
## [27] gridtext_0.1.5 igraph_1.5.1
## [29] sargent_1.0.1 SignacX_2.2.5
## [31] harmony_1.2.0 Rcpp_1.0.11
## [33] kableExtra_1.3.4 purrr_1.0.2
## [35] reticulate_1.34.0 RColorBrewer_1.1-3
## [37] cowplot_1.1.1 gridExtra_2.3
## [39] pheatmap_1.0.12 ggrepel_0.9.4
## [41] ggplot2_3.4.4 Seurat_5.0.1
## [43] SeuratObject_5.0.1 sp_2.1-2
## [45] dplyr_1.1.4 optparse_1.7.3
##
## loaded via a namespace (and not attached):
## [1] spatstat.sparse_3.0-3 bitops_1.0-7
## [3] httr_1.4.7 webshot_0.5.5
## [5] doParallel_1.0.17 tools_4.3.2
## [7] sctransform_0.4.1 utf8_1.2.4
## [9] R6_2.5.1 mgcv_1.9-0
## [11] lazyeval_0.2.2 uwot_0.1.16
## [13] ggdist_3.3.1 GetoptLong_1.0.5
## [15] withr_2.5.2 progressr_0.14.0
## [17] cli_3.6.1 spatstat.explore_3.2-5
## [19] fastDummies_1.7.3 labeling_0.4.3
## [21] sass_0.4.8 mvtnorm_1.2-4
## [23] spatstat.data_3.0-3 proxy_0.4-27
## [25] ggridges_0.5.4 pbapply_1.7-2
## [27] commonmark_1.9.0 systemfonts_1.0.5
## [29] R.utils_2.12.3 svglite_2.1.2
## [31] parallelly_1.36.0 rstudioapi_0.15.0
## [33] generics_0.1.3 shape_1.4.6
## [35] crosstalk_1.2.1 ica_1.0-3
## [37] spatstat.random_3.2-2 distributional_0.3.2
## [39] Matrix_1.6-4 fansi_1.0.6
## [41] DescTools_0.99.52 abind_1.4-5
## [43] R.methodsS3_1.8.2 lifecycle_1.0.4
## [45] yaml_2.3.7 SparseArray_1.2.2
## [47] Rtsne_0.17 promises_1.2.1
## [49] crayon_1.5.2 miniUI_0.1.1.1
## [51] lattice_0.22-5 pillar_1.9.0
## [53] knitr_1.45 rjson_0.2.21
## [55] boot_1.3-28.1 gld_2.6.6
## [57] future.apply_1.11.0 codetools_0.2-19
## [59] leiden_0.4.3.1 glue_1.6.2
## [61] vctrs_0.6.5 png_0.1-8
## [63] spam_2.10-0 neuralnet_1.44.2
## [65] cellranger_1.1.0 gtable_0.3.4
## [67] cachem_1.0.8 ks_1.14.1
## [69] xfun_0.41 S4Arrays_1.2.0
## [71] mime_0.12 pracma_2.4.4
## [73] survival_3.5-7 pbmcapply_1.5.1
## [75] iterators_1.0.14 statmod_1.5.0
## [77] ellipsis_0.3.2 fitdistrplus_1.1-11
## [79] ROCR_1.0-11 nlme_3.1-164
## [81] RcppAnnoy_0.0.21 bslib_0.6.1
## [83] irlba_2.3.5.1 KernSmooth_2.23-22
## [85] colorspace_2.1-0 Exact_3.2
## [87] tidyselect_1.2.0 compiler_4.3.2
## [89] rvest_1.0.3 expm_0.999-8
## [91] xml2_1.3.6 DelayedArray_0.28.0
## [93] scales_1.3.0 caTools_1.18.2
## [95] lmtest_0.9-40 stringr_1.5.1
## [97] digest_0.6.33 goftest_1.2-3
## [99] spatstat.utils_3.0-4 rmarkdown_2.25
## [101] RhpcBLASctl_0.23-42 XVector_0.42.0
## [103] htmltools_0.5.7 pkgconfig_2.0.3
## [105] highr_0.10 fastmap_1.1.1
## [107] rlang_1.1.2 GlobalOptions_0.1.2
## [109] htmlwidgets_1.6.4 shiny_1.8.0
## [111] jquerylib_0.1.4 farver_2.1.1
## [113] zoo_1.8-12 jsonlite_1.8.8
## [115] mclust_6.0.1 R.oo_1.25.0
## [117] RCurl_1.98-1.13 magrittr_2.0.3
## [119] GenomeInfoDbData_1.2.11 dotCall64_1.1-1
## [121] munsell_0.5.0 stringi_1.8.2
## [123] rootSolve_1.8.2.4 zlibbioc_1.48.0
## [125] MASS_7.3-60 plyr_1.8.9
## [127] parallel_4.3.2 listenv_0.9.0
## [129] lmom_3.0 deldir_2.0-2
## [131] splines_4.3.2 tensor_1.5
## [133] circlize_0.4.15 locfit_1.5-9.8
## [135] spatstat.geom_3.2-7 markdown_1.12
## [137] RcppHNSW_0.5.0 reshape2_1.4.4
## [139] evaluate_0.23 foreach_1.5.2
## [141] httpuv_1.6.13 RANN_2.6.1
## [143] tidyr_1.3.0 getopt_1.20.4
## [145] polyclip_1.10-6 future_1.33.0
## [147] clue_0.3-65 scattermore_1.2
## [149] xtable_1.8-4 e1071_1.7-14
## [151] RSpectra_0.16-1 later_1.3.2
## [153] viridisLite_0.4.2 class_7.3-22
## [155] tibble_3.2.1 cluster_2.1.6
## [157] globals_0.16.2