Saturation TCR analysis report

Published

May 28, 2024

Repertoire report generated with SatTCR

Analysis statistics

Sample Sequencing # clonotypes Shannon div Clonality D50
Depth Trim1 Complete Complete >= 5) Ratio Complete Complete >= 5) Complete Complete >= 5) Complete Complete >= 5)
run1_bio1_tech1 364,450 1 13,209 7,103 53.77% 86.75% 87.35% 13.25% 12.65% 1,048 655
run1_bio1_tech2 470,981 0 14,987 8,985 59.95% 86.62% 87.25% 13.38% 12.75% 1,155 802
run1_bio2_tech1 352,487 1 15,656 7,226 46.15% 87.20% 87.49% 12.80% 12.51% 1,203 618
run1_bio2_tech2 319,514 2 17,088 6,519 38.15% 86.67% 86.17% 13.33% 13.83% 1,300 503
run2_bio1_tech1 389,927 0 10,222 6,526 63.84% 85.89% 86.77% 14.11% 13.23% 762 574
run2_bio1_tech2 472,274 0 11,467 7,683 67.00% 86.03% 86.86% 13.97% 13.14% 857 674
run2_bio2_tech1 376,741 0 12,984 7,442 57.32% 86.80% 87.50% 13.20% 12.50% 965 635
run2_bio2_tech2 341,418 1 14,054 7,435 52.90% 86.56% 86.90% 13.44% 13.10% 1,066 624
run3_bio1_tech1 2,728,346 15 34,954 34,034 97.37% 88.93% 89.07% 11.07% 10.93% 3,387 3,373
run3_bio1_tech2 3,357,054 15 37,056 36,100 97.42% 88.81% 88.96% 11.19% 11.04% 3,517 3,504
run3_bio2_tech1 2,605,354 14 40,051 39,007 97.39% 89.46% 89.60% 10.54% 10.40% 4,206 4,188
run3_bio2_tech2 2,485,793 22 41,993 40,881 97.35% 89.31% 89.46% 10.69% 10.54% 4,701 4,679
1 # of trimmed sequences

Appendix

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
 os       Ubuntu 20.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       UTC
 date     2024-05-28
 pandoc   2.5 @ /usr/bin/ (via rmarkdown)
 quarto   1.4.549

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 dplyr       * 1.1.4   2023-11-17 [1] CRAN (R 4.4.0)
 forcats     * 1.0.0   2023-01-29 [2] RSPM (R 4.2.0)
 ggplot2     * 3.4.4   2023-10-12 [1] CRAN (R 4.4.0)
 gt          * 0.10.1  2024-01-17 [2] RSPM (R 4.3.2)
 lubridate   * 1.9.3   2023-09-27 [2] RSPM (R 4.3.0)
 magrittr    * 2.0.3   2022-03-30 [2] RSPM (R 4.2.0)
 purrr       * 1.0.2   2023-08-10 [2] RSPM (R 4.2.0)
 readr       * 2.1.5   2024-01-10 [2] RSPM (R 4.3.0)
 sessioninfo * 1.2.2   2021-12-06 [2] RSPM (R 4.2.0)
 stringr     * 1.5.1   2023-11-14 [2] RSPM (R 4.3.0)
 tibble      * 3.2.1   2023-03-20 [2] RSPM (R 4.3.0)
 tidyr       * 1.3.1   2024-01-24 [2] RSPM (R 4.3.0)
 tidyverse   * 2.0.0   2023-02-22 [2] RSPM (R 4.2.0)
 yaml        * 2.3.8   2023-12-11 [2] RSPM (R 4.3.0)

 [1] /usr/local/lib/R/site-library
 [2] /usr/lib/R/site-library
 [3] /usr/lib/R/library

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