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 | lung | sample_based | none | none | 750 | 20 | 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 | tissue | sample_id |
---|---|---|---|
001C | Control | Lung | S1 |
002C | Control | Lung | S2 |
003C | Control | Lung | S3 |
010I | IPF | Lung | S4 |
021I | IPF | Lung | S5 |
022I | IPF | Lung | S6 |
025I | IPF | Lung | S7 |
034C | Control | Lung | S8 |
034I | IPF | Lung | S9 |
040I | IPF | Lung | S10 |
041I | IPF | Lung | S11 |
051I | IPF | Lung | S12 |
052CO | COPD | Lung | S13 |
053I | IPF | Lung | S14 |
056CO | COPD | Lung | S15 |
063I | IPF | Lung | S16 |
065C | Control | Lung | S17 |
081C | Control | Lung | S18 |
084C | Control | Lung | S19 |
092C | Control | Lung | S20 |
098C | Control | Lung | S21 |
123I | IPF | Lung | S22 |
133C | Control | Lung | S23 |
135I | IPF | Lung | S24 |
1372C | Control | Lung | S25 |
137C | Control | Lung | S26 |
137CO | COPD | Lung | S27 |
138I | IPF | Lung | S28 |
145I | IPF | Lung | S29 |
152CO | COPD | Lung | S30 |
153CO | COPD | Lung | S31 |
157I | IPF | Lung | S32 |
158I | IPF | Lung | S33 |
160C | Control | Lung | S34 |
166I | IPF | Lung | S35 |
174I | IPF | Lung | S36 |
177I | IPF | Lung | S37 |
178CO | COPD | Lung | S38 |
179I | IPF | Lung | S39 |
184CO | COPD | Lung | S40 |
186CO | COPD | Lung | S41 |
192C | Control | Lung | S42 |
192CO | COPD | Lung | S43 |
193CO | COPD | Lung | S44 |
194CO | COPD | Lung | S45 |
207CO | COPD | Lung | S46 |
208C | Control | Lung | S47 |
209I | IPF | Lung | S48 |
210I | IPF | Lung | S49 |
212I | IPF | Lung | S50 |
214I | IPF | Lung | S51 |
217CO | COPD | Lung | S52 |
218C | Control | Lung | S53 |
221I | IPF | Lung | S54 |
222C | Control | Lung | S55 |
222I | IPF | Lung | S56 |
225I | IPF | Lung | S57 |
226C | Control | Lung | S58 |
228I | IPF | Lung | S59 |
235CO | COPD | Lung | S60 |
237CO | COPD | Lung | S61 |
238CO | COPD | Lung | S62 |
23CO | COPD | Lung | S63 |
244C | Control | Lung | S64 |
253C | Control | Lung | S65 |
296C | Control | Lung | S66 |
29I | IPF | Lung | S67 |
388C | Control | Lung | S68 |
396C | Control | Lung | S69 |
439C | Control | Lung | S70 |
454C | Control | Lung | S71 |
465C | Control | Lung | S72 |
47I | IPF | Lung | S73 |
483C | Control | Lung | S74 |
484C | Control | Lung | S75 |
49I | IPF | Lung | S76 |
59I | IPF | Lung | S77 |
8CO | COPD | Lung | S78 |
sample_id | pre_qc_gene | pre_qc_cell | post_qc_gene | post_qc_cell |
---|---|---|---|---|
S1 | 29,354 | 1,862 | 23,558 | 1,768 |
S2 | 27,688 | 700 | 21,742 | 643 |
S3 | 31,444 | 3,460 | 26,114 | 3,297 |
S4 | 33,738 | 4,867 | 28,627 | 4,696 |
S5 | 33,465 | 3,122 | 28,433 | 3,065 |
S6 | 33,798 | 4,843 | 28,577 | 4,724 |
S7 | 31,821 | 3,239 | 26,513 | 2,903 |
S8 | 27,129 | 706 | 21,039 | 670 |
S9 | 33,489 | 4,279 | 28,177 | 4,201 |
S10 | 34,451 | 4,949 | 29,216 | 4,753 |
S11 | 32,803 | 3,670 | 27,440 | 3,537 |
S12 | 34,820 | 6,839 | 29,671 | 6,655 |
S13 | 31,874 | 3,482 | 26,255 | 3,277 |
S14 | 33,540 | 3,718 | 28,091 | 3,633 |
S15 | 32,283 | 4,382 | 26,819 | 4,248 |
S16 | 30,810 | 3,292 | 25,177 | 3,076 |
S17 | 29,408 | 1,883 | 23,614 | 1,766 |
S18 | 26,641 | 982 | 20,086 | 844 |
S19 | 26,512 | 477 | 20,324 | 460 |
S20 | 29,393 | 4,319 | 23,673 | 3,719 |
S21 | 34,575 | 9,240 | 29,355 | 8,872 |
S22 | 31,449 | 1,851 | 25,811 | 1,804 |
S23 | 34,280 | 8,566 | 28,726 | 8,151 |
S24 | 35,814 | 6,368 | 30,139 | 6,162 |
S25 | 33,186 | 4,595 | 27,877 | 4,447 |
S26 | 29,008 | 999 | 23,169 | 966 |
S27 | 19,114 | 60 | 11,648 | 59 |
S28 | 35,024 | 3,665 | 29,644 | 3,582 |
S29 | 32,570 | 4,886 | 27,213 | 4,708 |
S30 | 33,694 | 4,923 | 27,698 | 4,738 |
S31 | 31,944 | 3,273 | 25,800 | 3,001 |
S32 | 35,620 | 7,063 | 30,600 | 6,874 |
S33 | 32,787 | 6,518 | 27,451 | 6,180 |
S34 | 31,563 | 4,541 | 26,068 | 4,216 |
S35 | 34,632 | 5,442 | 28,438 | 5,090 |
S36 | 33,360 | 5,876 | 27,951 | 5,652 |
S37 | 31,297 | 6,562 | 25,893 | 6,163 |
S38 | 32,146 | 8,879 | 26,734 | 8,313 |
S39 | 31,009 | 4,524 | 25,600 | 4,312 |
S40 | 34,421 | 6,514 | 28,623 | 6,256 |
S41 | 30,183 | 3,586 | 24,508 | 3,360 |
S42 | 33,156 | 4,028 | 27,672 | 3,856 |
S43 | 34,429 | 6,867 | 29,368 | 6,684 |
S44 | 33,148 | 6,802 | 27,991 | 6,570 |
S45 | 32,437 | 2,944 | 26,692 | 2,875 |
S46 | 31,689 | 3,165 | 26,240 | 3,089 |
S47 | 30,120 | 2,049 | 24,813 | 1,917 |
S48 | 33,496 | 4,592 | 28,260 | 4,451 |
S49 | 31,252 | 2,763 | 25,811 | 2,681 |
S50 | 35,452 | 4,496 | 29,806 | 4,368 |
S51 | 31,327 | 957 | 25,018 | 933 |
S52 | 33,140 | 2,573 | 26,869 | 2,512 |
S53 | 35,044 | 4,823 | 29,223 | 4,489 |
S54 | 34,779 | 5,330 | 28,847 | 5,097 |
S55 | 35,016 | 10,110 | 29,962 | 9,732 |
S56 | 35,642 | 8,641 | 30,670 | 8,383 |
S57 | 36,373 | 12,085 | 31,239 | 11,607 |
S58 | 34,525 | 10,736 | 28,697 | 9,939 |
S59 | 32,972 | 3,215 | 27,687 | 3,091 |
S60 | 31,642 | 4,176 | 26,016 | 4,038 |
S61 | 33,122 | 3,566 | 27,516 | 3,477 |
S62 | 30,877 | 1,961 | 25,453 | 1,921 |
S63 | 31,139 | 1,850 | 25,403 | 1,728 |
S64 | 23,437 | 166 | 17,010 | 166 |
S65 | 28,909 | 945 | 23,356 | 895 |
S66 | 32,664 | 3,303 | 27,225 | 3,184 |
S67 | 30,511 | 1,263 | 25,031 | 1,207 |
S68 | 29,417 | 2,287 | 23,499 | 2,075 |
S69 | 25,865 | 1,268 | 20,025 | 1,210 |
S70 | 33,836 | 7,197 | 28,560 | 6,948 |
S71 | 27,765 | 1,163 | 21,982 | 1,139 |
S72 | 31,870 | 2,622 | 26,648 | 2,559 |
S73 | 32,062 | 2,463 | 26,409 | 2,381 |
S74 | 30,179 | 2,166 | 24,470 | 1,876 |
S75 | 27,998 | 1,110 | 22,017 | 1,080 |
S76 | 33,849 | 4,624 | 28,590 | 4,530 |
S77 | 30,569 | 1,167 | 24,922 | 1,153 |
S78 | 27,654 | 453 | 21,757 | 444 |
Vales are post-QC.
sample_id | min | 0% | 25% | 50% | 75% | 100% | max |
---|---|---|---|---|---|---|---|
S1 | 999 | 999 | 2,260 | 3,960 | 6,670 | 28,583 | 28,583 |
S2 | 1,009 | 1,009 | 4,343 | 7,013 | 10,965 | 36,524 | 36,524 |
S3 | 1,001 | 1,001 | 3,035 | 5,906 | 11,330 | 48,220 | 48,220 |
S4 | 1,006 | 1,006 | 3,276 | 5,678 | 9,526 | 85,160 | 85,160 |
S5 | 1,001 | 1,001 | 2,930 | 5,083 | 9,528 | 117,292 | 117,292 |
S6 | 1,002 | 1,002 | 2,749 | 4,752 | 8,258 | 144,295 | 144,295 |
S7 | 1,016 | 1,016 | 3,658 | 6,461 | 10,401 | 95,551 | 95,551 |
S8 | 998 | 998 | 2,626 | 4,540 | 8,403 | 29,012 | 29,012 |
S9 | 1,002 | 1,002 | 2,700 | 4,995 | 9,258 | 85,545 | 85,545 |
S10 | 1,003 | 1,003 | 3,458 | 6,118 | 10,181 | 110,848 | 110,848 |
S11 | 999 | 999 | 3,836 | 6,841 | 11,259 | 65,753 | 65,753 |
S12 | 1,004 | 1,004 | 2,716 | 4,381 | 7,275 | 94,428 | 94,428 |
S13 | 998 | 998 | 2,419 | 3,723 | 5,245 | 36,415 | 36,415 |
S14 | 1,002 | 1,002 | 3,172 | 5,978 | 11,215 | 69,783 | 69,783 |
S15 | 1,001 | 1,001 | 2,045 | 3,125 | 5,235 | 29,610 | 29,610 |
S16 | 1,000 | 1,000 | 2,695 | 4,980 | 8,972 | 52,572 | 52,572 |
S17 | 1,001 | 1,001 | 2,109 | 3,592 | 5,638 | 34,779 | 34,779 |
S18 | 1,000 | 1,000 | 2,080 | 3,200 | 4,854 | 26,723 | 26,723 |
S19 | 999 | 999 | 2,892 | 5,198 | 8,992 | 21,290 | 21,290 |
S20 | 1,008 | 1,008 | 4,478 | 7,731 | 10,696 | 23,807 | 23,807 |
S21 | 999 | 999 | 2,035 | 4,008 | 9,015 | 55,865 | 55,865 |
S22 | 1,002 | 1,002 | 3,860 | 6,462 | 11,939 | 73,686 | 73,686 |
S23 | 1,000 | 1,000 | 3,278 | 6,060 | 9,692 | 63,791 | 63,791 |
S24 | 999 | 999 | 3,528 | 5,906 | 9,574 | 70,613 | 70,613 |
S25 | 1,001 | 1,001 | 2,678 | 4,933 | 8,828 | 68,838 | 68,838 |
S26 | 1,009 | 1,009 | 4,017 | 6,090 | 9,838 | 43,933 | 43,933 |
S27 | 860 | 860 | 2,086 | 3,681 | 6,453 | 29,439 | 29,439 |
S28 | 1,006 | 1,006 | 3,523 | 6,809 | 11,809 | 91,304 | 91,304 |
S29 | 1,000 | 1,000 | 2,702 | 4,784 | 9,261 | 70,500 | 70,500 |
S30 | 1,000 | 1,000 | 1,723 | 3,366 | 5,837 | 91,268 | 91,268 |
S31 | 999 | 999 | 2,153 | 3,495 | 5,187 | 27,794 | 27,794 |
S32 | 1,001 | 1,001 | 3,565 | 6,032 | 10,275 | 122,498 | 122,498 |
S33 | 1,001 | 1,001 | 2,429 | 4,680 | 8,867 | 44,610 | 44,610 |
S34 | 1,001 | 1,001 | 3,281 | 5,624 | 7,876 | 39,533 | 39,533 |
S35 | 999 | 999 | 2,153 | 3,632 | 6,469 | 61,348 | 61,348 |
S36 | 1,000 | 1,000 | 3,342 | 5,692 | 9,669 | 63,716 | 63,716 |
S37 | 1,000 | 1,000 | 1,596 | 3,455 | 7,782 | 44,445 | 44,445 |
S38 | 999 | 999 | 1,314 | 1,869 | 3,420 | 68,943 | 68,943 |
S39 | 1,005 | 1,005 | 2,857 | 5,494 | 9,209 | 43,864 | 43,864 |
S40 | 1,001 | 1,001 | 1,935 | 2,930 | 5,218 | 49,868 | 49,868 |
S41 | 999 | 999 | 2,651 | 4,898 | 8,061 | 42,361 | 42,361 |
S42 | 1,003 | 1,003 | 2,999 | 5,314 | 8,986 | 176,969 | 176,969 |
S43 | 1,001 | 1,001 | 2,774 | 4,866 | 12,662 | 76,773 | 76,773 |
S44 | 999 | 999 | 1,978 | 2,879 | 5,112 | 97,600 | 97,600 |
S45 | 1,008 | 1,008 | 2,428 | 4,597 | 9,152 | 45,880 | 45,880 |
S46 | 1,000 | 1,000 | 2,483 | 3,702 | 5,525 | 41,955 | 41,955 |
S47 | 1,009 | 1,009 | 2,575 | 4,022 | 6,493 | 66,332 | 66,332 |
S48 | 1,000 | 1,000 | 3,296 | 5,780 | 10,426 | 83,283 | 83,283 |
S49 | 997 | 997 | 3,018 | 5,571 | 9,150 | 46,239 | 46,239 |
S50 | 1,003 | 1,003 | 3,391 | 6,142 | 11,310 | 80,338 | 80,338 |
S51 | 1,000 | 1,000 | 2,881 | 4,908 | 7,532 | 33,429 | 33,429 |
S52 | 999 | 999 | 2,305 | 3,637 | 5,533 | 45,239 | 45,239 |
S53 | 1,001 | 1,001 | 2,213 | 3,684 | 6,216 | 88,327 | 88,327 |
S54 | 1,000 | 1,000 | 2,809 | 5,263 | 9,346 | 63,803 | 63,803 |
S55 | 1,000 | 1,000 | 2,483 | 4,098 | 8,010 | 59,527 | 59,527 |
S56 | 1,000 | 1,000 | 3,074 | 5,868 | 10,848 | 83,601 | 83,601 |
S57 | 1,000 | 1,000 | 3,524 | 6,325 | 10,344 | 96,840 | 96,840 |
S58 | 999 | 999 | 2,054 | 3,270 | 5,111 | 46,032 | 46,032 |
S59 | 1,003 | 1,003 | 2,300 | 4,090 | 7,594 | 97,063 | 97,063 |
S60 | 999 | 999 | 1,968 | 3,200 | 5,175 | 57,355 | 57,355 |
S61 | 1,002 | 1,002 | 2,198 | 3,524 | 5,623 | 34,506 | 34,506 |
S62 | 1,004 | 1,004 | 3,764 | 6,822 | 11,957 | 90,454 | 90,454 |
S63 | 1,007 | 1,007 | 4,976 | 10,205 | 18,235 | 71,088 | 71,088 |
S64 | 998 | 998 | 1,485 | 2,280 | 4,821 | 23,338 | 23,338 |
S65 | 1,020 | 1,020 | 3,653 | 6,518 | 11,342 | 65,342 | 65,342 |
S66 | 1,001 | 1,001 | 2,692 | 4,885 | 8,016 | 35,083 | 35,083 |
S67 | 1,063 | 1,063 | 6,320 | 11,091 | 17,156 | 129,605 | 129,605 |
S68 | 997 | 997 | 1,757 | 2,892 | 4,826 | 24,265 | 24,265 |
S69 | 996 | 996 | 1,304 | 2,032 | 3,794 | 17,131 | 17,131 |
S70 | 1,000 | 1,000 | 2,289 | 3,684 | 7,438 | 81,946 | 81,946 |
S71 | 1,001 | 1,001 | 2,890 | 4,253 | 7,294 | 25,865 | 25,865 |
S72 | 999 | 999 | 3,130 | 4,534 | 11,779 | 43,030 | 43,030 |
S73 | 1,001 | 1,001 | 3,879 | 6,459 | 10,747 | 89,115 | 89,115 |
S74 | 1,005 | 1,005 | 3,252 | 5,728 | 8,937 | 25,534 | 25,534 |
S75 | 1,020 | 1,020 | 3,022 | 4,889 | 10,944 | 46,395 | 46,395 |
S76 | 1,000 | 1,000 | 3,009 | 4,720 | 7,361 | 74,794 | 74,794 |
S77 | 1,006 | 1,006 | 3,554 | 5,732 | 11,082 | 88,080 | 88,080 |
S78 | 1,028 | 1,028 | 3,992 | 6,765 | 11,129 | 47,669 | 47,669 |
Vales are post-QC.
sample_id | min | 0% | 25% | 50% | 75% | 100% | max |
---|---|---|---|---|---|---|---|
S1 | 540 | 540 | 1,180 | 1,752 | 2,511 | 6,761 | 6,761 |
S2 | 638 | 638 | 1,950 | 2,691 | 3,560 | 6,929 | 6,929 |
S3 | 546 | 546 | 1,446 | 2,281 | 3,396 | 7,604 | 7,604 |
S4 | 541 | 541 | 1,492 | 2,231 | 3,151 | 12,666 | 12,666 |
S5 | 534 | 534 | 1,416 | 2,051 | 3,172 | 13,283 | 13,283 |
S6 | 514 | 514 | 1,320 | 1,965 | 2,857 | 12,752 | 12,752 |
S7 | 563 | 563 | 1,698 | 2,513 | 3,373 | 10,586 | 10,586 |
S8 | 411 | 411 | 1,345 | 1,952 | 2,975 | 6,108 | 6,108 |
S9 | 490 | 490 | 1,336 | 2,068 | 3,026 | 10,845 | 10,845 |
S10 | 251 | 251 | 1,555 | 2,332 | 3,274 | 11,448 | 11,448 |
S11 | 529 | 529 | 1,696 | 2,488 | 3,362 | 10,225 | 10,225 |
S12 | 504 | 504 | 1,304 | 1,842 | 2,635 | 10,267 | 10,267 |
S13 | 556 | 556 | 1,235 | 1,636 | 2,050 | 8,703 | 8,703 |
S14 | 484 | 484 | 1,517 | 2,350 | 3,470 | 11,051 | 11,051 |
S15 | 521 | 521 | 1,104 | 1,516 | 2,225 | 7,196 | 7,196 |
S16 | 542 | 542 | 1,358 | 2,088 | 2,902 | 7,850 | 7,850 |
S17 | 549 | 549 | 1,135 | 1,680 | 2,340 | 8,305 | 8,305 |
S18 | 472 | 472 | 1,044 | 1,462 | 1,974 | 5,751 | 5,751 |
S19 | 438 | 438 | 1,494 | 2,264 | 3,272 | 5,969 | 5,969 |
S20 | 571 | 571 | 1,877 | 2,593 | 3,133 | 5,312 | 5,312 |
S21 | 510 | 510 | 1,128 | 1,774 | 2,943 | 8,580 | 8,580 |
S22 | 590 | 590 | 1,609 | 2,230 | 3,414 | 8,369 | 8,369 |
S23 | 541 | 541 | 1,485 | 2,223 | 2,944 | 7,820 | 7,820 |
S24 | 556 | 556 | 1,524 | 2,210 | 3,098 | 11,119 | 11,119 |
S25 | 518 | 518 | 1,315 | 1,991 | 2,860 | 9,192 | 9,192 |
S26 | 488 | 488 | 1,751 | 2,246 | 3,095 | 7,538 | 7,538 |
S27 | 460 | 460 | 987 | 1,626 | 2,733 | 5,154 | 5,154 |
S28 | 395 | 395 | 1,592 | 2,514 | 3,579 | 11,576 | 11,576 |
S29 | 547 | 547 | 1,306 | 1,934 | 2,928 | 9,291 | 9,291 |
S30 | 424 | 424 | 969 | 1,563 | 2,300 | 11,003 | 11,003 |
S31 | 464 | 464 | 1,132 | 1,620 | 2,125 | 7,579 | 7,579 |
S32 | 406 | 406 | 1,602 | 2,313 | 3,266 | 13,055 | 13,055 |
S33 | 543 | 543 | 1,196 | 1,940 | 2,881 | 9,555 | 9,555 |
S34 | 514 | 514 | 1,545 | 2,279 | 2,821 | 9,486 | 9,486 |
S35 | 467 | 467 | 1,134 | 1,670 | 2,444 | 8,701 | 8,701 |
S36 | 492 | 492 | 1,470 | 2,200 | 3,070 | 9,920 | 9,920 |
S37 | 419 | 419 | 861 | 1,519 | 2,528 | 8,134 | 8,134 |
S38 | 408 | 408 | 825 | 1,091 | 1,682 | 9,646 | 9,646 |
S39 | 504 | 504 | 1,307 | 2,032 | 2,827 | 7,537 | 7,537 |
S40 | 534 | 534 | 1,047 | 1,416 | 2,099 | 10,328 | 10,328 |
S41 | 530 | 530 | 1,275 | 1,986 | 2,755 | 8,455 | 8,455 |
S42 | 472 | 472 | 1,433 | 2,106 | 2,995 | 12,124 | 12,124 |
S43 | 282 | 282 | 1,295 | 1,952 | 3,506 | 9,891 | 9,891 |
S44 | 338 | 338 | 1,060 | 1,382 | 2,029 | 9,964 | 9,964 |
S45 | 548 | 548 | 1,252 | 1,983 | 3,138 | 8,986 | 8,986 |
S46 | 438 | 438 | 1,231 | 1,653 | 2,131 | 8,388 | 8,388 |
S47 | 573 | 573 | 1,288 | 1,819 | 2,501 | 11,885 | 11,885 |
S48 | 492 | 492 | 1,483 | 2,245 | 3,220 | 10,266 | 10,266 |
S49 | 536 | 536 | 1,356 | 2,074 | 2,866 | 8,358 | 8,358 |
S50 | 496 | 496 | 1,533 | 2,434 | 3,591 | 12,566 | 12,566 |
S51 | 585 | 585 | 1,447 | 2,185 | 3,107 | 7,848 | 7,848 |
S52 | 490 | 490 | 1,132 | 1,567 | 2,080 | 10,249 | 10,249 |
S53 | 482 | 482 | 1,161 | 1,698 | 2,406 | 13,173 | 13,173 |
S54 | 560 | 560 | 1,386 | 2,145 | 3,105 | 11,178 | 11,178 |
S55 | 377 | 377 | 1,233 | 1,752 | 2,743 | 8,348 | 8,348 |
S56 | 508 | 508 | 1,450 | 2,271 | 3,340 | 11,315 | 11,315 |
S57 | 508 | 508 | 1,639 | 2,424 | 3,284 | 11,335 | 11,335 |
S58 | 484 | 484 | 1,034 | 1,422 | 1,931 | 9,452 | 9,452 |
S59 | 293 | 293 | 1,182 | 1,779 | 2,780 | 10,951 | 10,951 |
S60 | 351 | 351 | 995 | 1,494 | 2,151 | 9,683 | 9,683 |
S61 | 468 | 468 | 1,147 | 1,613 | 2,226 | 7,794 | 7,794 |
S62 | 577 | 577 | 1,549 | 2,373 | 3,504 | 10,509 | 10,509 |
S63 | 573 | 573 | 1,940 | 3,084 | 4,254 | 7,581 | 7,581 |
S64 | 648 | 648 | 945 | 1,344 | 2,231 | 5,604 | 5,604 |
S65 | 597 | 597 | 1,700 | 2,460 | 3,462 | 8,489 | 8,489 |
S66 | 519 | 519 | 1,420 | 2,120 | 3,026 | 7,743 | 7,743 |
S67 | 521 | 521 | 2,276 | 3,278 | 4,170 | 11,178 | 11,178 |
S68 | 522 | 522 | 1,014 | 1,451 | 2,066 | 5,474 | 5,474 |
S69 | 471 | 471 | 793 | 1,129 | 1,775 | 4,978 | 4,978 |
S70 | 456 | 456 | 1,217 | 1,734 | 2,890 | 9,222 | 9,222 |
S71 | 504 | 504 | 1,358 | 1,823 | 2,614 | 6,506 | 6,506 |
S72 | 527 | 527 | 1,585 | 2,068 | 3,488 | 8,484 | 8,484 |
S73 | 526 | 526 | 1,714 | 2,460 | 3,355 | 9,355 | 9,355 |
S74 | 470 | 470 | 1,612 | 2,464 | 3,257 | 6,467 | 6,467 |
S75 | 439 | 439 | 1,396 | 1,955 | 3,262 | 6,739 | 6,739 |
S76 | 365 | 365 | 1,410 | 1,944 | 2,713 | 10,134 | 10,134 |
S77 | 620 | 620 | 1,646 | 2,187 | 3,565 | 8,879 | 8,879 |
S78 | 492 | 492 | 1,804 | 2,486 | 3,604 | 7,299 | 7,299 |
Vales are post-QC.
sample_id | min | 0% | 25% | 50% | 75% | 100% | max |
---|---|---|---|---|---|---|---|
S1 | 0.37 | 0.37 | 3.99 | 5.80 | 9.34 | 19.97 | 19.97 |
S2 | 0.33 | 0.33 | 3.85 | 7.14 | 11.55 | 19.81 | 19.81 |
S3 | 0.21 | 0.21 | 3.00 | 4.78 | 8.27 | 19.99 | 19.99 |
S4 | 0.25 | 0.25 | 3.85 | 5.78 | 9.42 | 19.98 | 19.98 |
S5 | 0.19 | 0.19 | 3.39 | 5.61 | 8.99 | 19.87 | 19.87 |
S6 | 0.16 | 0.16 | 3.07 | 4.96 | 8.29 | 19.97 | 19.97 |
S7 | 0.44 | 0.44 | 4.91 | 7.51 | 10.96 | 19.98 | 19.98 |
S8 | 0.44 | 0.44 | 3.90 | 6.06 | 9.24 | 19.91 | 19.91 |
S9 | 0.00 | 0.00 | 3.02 | 4.62 | 7.60 | 19.94 | 19.94 |
S10 | 0.17 | 0.17 | 3.98 | 6.53 | 10.10 | 20.00 | 20.00 |
S11 | 0.41 | 0.41 | 3.46 | 5.54 | 8.57 | 20.00 | 20.00 |
S12 | 0.28 | 0.28 | 4.42 | 7.06 | 10.54 | 19.98 | 19.98 |
S13 | 0.00 | 0.00 | 1.97 | 2.96 | 5.03 | 19.93 | 19.93 |
S14 | 0.48 | 0.48 | 3.26 | 5.15 | 8.29 | 19.96 | 19.96 |
S15 | 0.22 | 0.22 | 2.18 | 3.56 | 7.31 | 19.97 | 19.97 |
S16 | 0.29 | 0.29 | 3.17 | 5.07 | 8.81 | 20.00 | 20.00 |
S17 | 0.31 | 0.31 | 3.43 | 4.85 | 7.27 | 19.86 | 19.86 |
S18 | 0.60 | 0.60 | 5.91 | 9.27 | 12.99 | 19.91 | 19.91 |
S19 | 0.81 | 0.81 | 4.43 | 6.31 | 10.09 | 19.90 | 19.90 |
S20 | 0.20 | 0.20 | 4.38 | 6.33 | 9.10 | 19.99 | 19.99 |
S21 | 0.00 | 0.00 | 2.21 | 3.35 | 6.02 | 19.97 | 19.97 |
S22 | 0.57 | 0.57 | 2.84 | 4.44 | 7.21 | 19.95 | 19.95 |
S23 | 0.00 | 0.00 | 2.80 | 3.78 | 5.57 | 19.89 | 19.89 |
S24 | 0.32 | 0.32 | 4.23 | 5.95 | 8.95 | 19.96 | 19.96 |
S25 | 0.12 | 0.12 | 3.64 | 5.12 | 7.45 | 20.00 | 20.00 |
S26 | 0.68 | 0.68 | 3.39 | 5.08 | 7.22 | 19.81 | 19.81 |
S27 | 1.93 | 1.93 | 3.53 | 5.00 | 9.02 | 19.44 | 19.44 |
S28 | 0.40 | 0.40 | 3.70 | 5.09 | 7.53 | 19.99 | 19.99 |
S29 | 0.17 | 0.17 | 3.41 | 4.69 | 6.88 | 19.69 | 19.69 |
S30 | 0.19 | 0.19 | 2.24 | 3.38 | 4.77 | 19.87 | 19.87 |
S31 | 0.21 | 0.21 | 4.24 | 6.75 | 10.63 | 19.98 | 19.98 |
S32 | 0.20 | 0.20 | 3.51 | 5.40 | 8.20 | 19.93 | 19.93 |
S33 | 0.04 | 0.04 | 2.62 | 3.85 | 6.22 | 19.97 | 19.97 |
S34 | 0.18 | 0.18 | 4.59 | 7.12 | 11.56 | 20.00 | 20.00 |
S35 | 0.00 | 0.00 | 2.77 | 3.87 | 5.64 | 19.98 | 19.98 |
S36 | 0.28 | 0.28 | 2.86 | 4.58 | 7.60 | 19.99 | 19.99 |
S37 | 0.00 | 0.00 | 5.12 | 7.59 | 10.76 | 19.98 | 19.98 |
S38 | 0.29 | 0.29 | 2.80 | 4.25 | 6.34 | 19.95 | 19.95 |
S39 | 0.40 | 0.40 | 4.06 | 5.78 | 8.56 | 19.85 | 19.85 |
S40 | 0.10 | 0.10 | 2.14 | 2.95 | 4.62 | 19.92 | 19.92 |
S41 | 0.86 | 0.86 | 4.54 | 8.45 | 12.73 | 20.00 | 20.00 |
S42 | 0.16 | 0.16 | 4.03 | 6.01 | 9.07 | 20.00 | 20.00 |
S43 | 0.13 | 0.13 | 2.72 | 4.67 | 7.56 | 19.96 | 19.96 |
S44 | 0.18 | 0.18 | 2.66 | 3.63 | 6.37 | 19.99 | 19.99 |
S45 | 0.54 | 0.54 | 3.87 | 5.87 | 9.22 | 19.97 | 19.97 |
S46 | 0.13 | 0.13 | 2.22 | 3.67 | 6.57 | 19.85 | 19.85 |
S47 | 0.24 | 0.24 | 5.38 | 7.90 | 11.66 | 19.94 | 19.94 |
S48 | 0.36 | 0.36 | 3.70 | 5.69 | 9.15 | 19.99 | 19.99 |
S49 | 0.43 | 0.43 | 5.35 | 8.17 | 12.39 | 19.98 | 19.98 |
S50 | 0.05 | 0.05 | 3.85 | 5.79 | 8.84 | 19.99 | 19.99 |
S51 | 0.19 | 0.19 | 4.39 | 7.11 | 11.33 | 19.96 | 19.96 |
S52 | 0.21 | 0.21 | 3.02 | 4.82 | 7.72 | 19.99 | 19.99 |
S53 | 0.18 | 0.18 | 2.60 | 3.64 | 5.62 | 19.95 | 19.95 |
S54 | 0.18 | 0.18 | 3.54 | 5.30 | 8.04 | 19.97 | 19.97 |
S55 | 0.13 | 0.13 | 3.41 | 5.64 | 8.65 | 19.99 | 19.99 |
S56 | 0.04 | 0.04 | 3.21 | 4.90 | 7.69 | 19.98 | 19.98 |
S57 | 0.03 | 0.03 | 2.82 | 4.27 | 6.76 | 19.97 | 19.97 |
S58 | 0.30 | 0.30 | 2.77 | 3.59 | 4.87 | 19.97 | 19.97 |
S59 | 0.45 | 0.45 | 3.19 | 5.07 | 8.29 | 19.98 | 19.98 |
S60 | 0.17 | 0.17 | 3.18 | 5.90 | 9.72 | 19.98 | 19.98 |
S61 | 0.06 | 0.06 | 2.06 | 3.09 | 5.00 | 19.71 | 19.71 |
S62 | 0.39 | 0.39 | 3.52 | 7.17 | 11.53 | 19.98 | 19.98 |
S63 | 0.55 | 0.55 | 3.17 | 4.54 | 6.77 | 19.87 | 19.87 |
S64 | 1.43 | 1.43 | 2.50 | 3.63 | 5.38 | 19.25 | 19.25 |
S65 | 0.68 | 0.68 | 3.77 | 5.12 | 7.67 | 19.85 | 19.85 |
S66 | 0.08 | 0.08 | 2.98 | 4.80 | 7.86 | 19.94 | 19.94 |
S67 | 0.89 | 0.89 | 4.70 | 6.92 | 9.81 | 19.96 | 19.96 |
S68 | 0.70 | 0.70 | 4.10 | 6.05 | 8.34 | 19.97 | 19.97 |
S69 | 0.29 | 0.29 | 4.45 | 7.64 | 11.96 | 19.99 | 19.99 |
S70 | 0.00 | 0.00 | 2.64 | 4.27 | 6.95 | 19.82 | 19.82 |
S71 | 0.17 | 0.17 | 3.71 | 6.04 | 9.75 | 19.91 | 19.91 |
S72 | 0.00 | 0.00 | 1.58 | 2.22 | 3.30 | 19.68 | 19.68 |
S73 | 0.38 | 0.38 | 4.46 | 7.25 | 10.92 | 19.88 | 19.88 |
S74 | 0.61 | 0.61 | 4.79 | 7.47 | 11.94 | 19.99 | 19.99 |
S75 | 1.05 | 1.05 | 3.94 | 5.77 | 9.91 | 19.98 | 19.98 |
S76 | 0.40 | 0.40 | 3.63 | 5.74 | 8.82 | 19.96 | 19.96 |
S77 | 0.91 | 0.91 | 2.87 | 4.39 | 7.01 | 19.69 | 19.69 |
S78 | 0.47 | 0.47 | 2.22 | 3.58 | 5.82 | 19.92 | 19.92 |
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.
## [1] "No overlaps among samples' barcodes."
Fraction (%) of barcodes shared between pairs of samples post-QC.
## [1] "No overlaps among samples' barcodes."
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 | 860 | 860 | 2,545 | 4,595 | 8,401 | 176,969 | 176,969 |
Gene per cell | 251 | 251 | 1,270 | 1,919 | 2,863 | 13,283 | 13,283 |
Mitochondrial (%) per cell | 0.00 | 0.00 | 3.09 | 4.89 | 8.03 | 20.00 | 20.00 |
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