flashier_pbmc_purified
Matthew Stephens
2024-04-04
Last updated: 2024-04-05
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Knit directory: misc/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 8b7bab0 | Matthew Stephens | 2024-04-05 | workflowr::wflow_publish("flashier_pbmc_purified.Rmd") |
| html | 059e85c | Matthew Stephens | 2024-04-04 | Build site. |
| Rmd | cb16e70 | Matthew Stephens | 2024-04-04 | workflowr::wflow_publish("flashier_pbmc_purified.Rmd") |
Introduction
I run flashier (sparse EBNMF) on the purified pbmcs. I use some code from Eric Weine to plot the results.
library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(tidyr)
library(purrr)
library(stringr)
library(Matrix)
Attaching package: 'Matrix'The following objects are masked from 'package:tidyr':
expand, pack, unpacklibrary(flashier)Loading required package: ebnmLoading required package: magrittr
Attaching package: 'magrittr'The following object is masked from 'package:purrr':
set_namesThe following object is masked from 'package:tidyr':
extractlibrary(ggplot2)Load the data (in a sparse matrix called counts)
load("../data/pbmc_purified.RData")lcounts = counts
lcounts@x = log(counts@x + 1)Run flashier
fit1 = flash(lcounts,S = 0.01, ebnm_fn = ebnm_point_exponential, var_type = 2)Adding factor 1 to flash object...
Adding factor 2 to flash object...
Adding factor 3 to flash object...
Adding factor 4 to flash object...
Adding factor 5 to flash object...
Adding factor 6 to flash object...
Adding factor 7 to flash object...
Adding factor 8 to flash object...
Adding factor 9 to flash object...
Adding factor 10 to flash object...
Adding factor 11 to flash object...
Adding factor 12 to flash object...
Adding factor 13 to flash object...
Adding factor 14 to flash object...
Adding factor 15 to flash object...
Adding factor 16 to flash object...
Adding factor 17 to flash object...
Adding factor 18 to flash object...
Adding factor 19 to flash object...
Factor doesn't significantly increase objective and won't be added.
Wrapping up...
Done.
Nullchecking 18 factors...
Done.saveRDS(fit1,file='../output/fit.nn.pbmc.purified.rds')Note that the first factor is “intercept-like”, capturing library size and some kind of background expression,
plot(fit1$L_pm[,1],rowSums(lcounts),main="loadings for factor 1 vs rowSums of lcounts")
| Version | Author | Date |
|---|---|---|
| 059e85c | Matthew Stephens | 2024-04-04 |
Here I am using Eric’s code to plot a heatmap of the results, ordered by cell type
FF_log1p = fit1$L_pm
FF_log1p <- scale(FF_log1p, center = FALSE, scale = apply(FF_log1p, 2, max))
colnames(FF_log1p) <- paste0("k", 1:ncol(FF_log1p))
cell.type <- samples$celltype
# Downsample the number of cells and sort them using tSNE.
set.seed(8675309)
cell.idx <- numeric(0)
cell.types <- levels(cell.type)
for (i in 1:length(cell.types)) {
which.idx <- which(cell.type == cell.types[i])
# Downsample common cell types.
if (length(which.idx) > 1250) {
which.idx <- sample(which.idx, 1250)
}
# Don't include rare cell types.
if (length(which.idx) > 20) {
# Sort using tsne.
tsne.res <- Rtsne::Rtsne(
FF_log1p[which.idx, ],
dims = 1,
pca = FALSE,
normalize = FALSE,
perplexity = min(100, floor((length(which.idx) - 1) / 3) - 1),
theta = 0.1,
max_iter = 1000,
eta = 200,
check_duplicates = FALSE
)$Y[, 1]
which.idx <- which.idx[order(tsne.res)]
cell.idx <- c(cell.idx, which.idx)
}
}
cell.type <- cell.type[cell.idx]
cell.type <- droplevels(cell.type)
FF_log1p <- FF_log1p[cell.idx, ]
make.heatmap.tib <- function(FF) {
tib <- as_tibble(scale(FF, center = FALSE, scale = apply(FF, 2, max))) %>%
mutate(Cell.type = cell.type) %>%
arrange(Cell.type) %>%
mutate(Cell.idx = row_number())
tib <- tib %>%
pivot_longer(
-c(Cell.idx, Cell.type),
names_to = "Factor",
values_to = "Loading",
values_drop_na = TRUE
) %>%
mutate(Factor = as.numeric(str_extract(Factor, "[0-9]+")))
return(tib)
}
log1p_tib <- make.heatmap.tib(FF_log1p)
heatmap.tib = log1p_tib
tib <- heatmap.tib %>%
group_by(Cell.type, Cell.idx) %>%
summarize()`summarise()` has grouped output by 'Cell.type'. You can override using the
`.groups` argument.cell_type_breaks <- c(1, which(tib$Cell.type[-1] != tib$Cell.type[-nrow(tib)]))
label_pos <- cell_type_breaks / 2 + c(cell_type_breaks[-1], nrow(tib)) / 2
plt <- ggplot(heatmap.tib, aes(x = Factor, y = -Cell.idx, fill = Loading)) +
geom_tile() +
scale_fill_gradient(low = "white", high = "firebrick") +
labs(y = "") +
scale_y_continuous(breaks = -label_pos,
minor_breaks = NULL,
labels = levels(cell.type)) +
scale_x_continuous(breaks = seq(0, 30, 5)) +
theme_minimal() +
geom_hline(yintercept = -cell_type_breaks, size = 0.1) +
theme(legend.position = "none",
strip.text = element_text(size = 16)) Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.plt
| Version | Author | Date |
|---|---|---|
| 059e85c | Matthew Stephens | 2024-04-04 |
List driving genes:
for(k in 1:18){
print(paste0("factor ",k))
key = fit1$F_pm[,k]>1
vals = fit1$F_pm[key,k]
print(genes$symbol[key][order(vals,decreasing =TRUE)])
}[1] "factor 1"
[1] "MALAT1" "RPL13" "RPS2" "RPL10" "RPL13A" "RPS6"
[7] "RPS18" "B2M" "RPS4X" "RPL3" "RPS27" "RPS3"
[13] "RPS14" "TMSB4X" "RPL32" "RPS19" "RPL11" "RPS12"
[19] "RPL18A" "RPLP1" "RPL19" "RPLP2" "RPL21" "RPS3A"
[25] "RPS15" "RPS15A" "RPS27A" "RPL15" "RPL28" "RPL12"
[31] "RPL23A" "RPL18" "RPL31" "RPS8" "TMSB10" "RPL34"
[37] "RPS23" "RPL27A" "RPL26" "RPS9" "RPL6" "RPL8"
[43] "RPL29" "RPL7" "RPL10A" "RPS7" "RPL9" "RPL35A"
[49] "RPS5" "RPS16" "RPS25" "RPL14" "MT-CO1" "RPS13"
[55] "RPL30" "TPT1" "RPL35" "RPL5" "RPL36" "GNB2L1"
[61] "HLA-B" "ACTB" "RPL7A" "EEF1A1" "FAU" "RPS28"
[67] "RPSA" "FTL" "PTMA" "HLA-A" "RPS20" "UBA52"
[73] "RPLP0" "RPL4" "MT-CO3" "RPL37A" "FTH1" "NACA"
[79] "RPS24" "RPL37" "RPL27" "EIF1" "EEF1D" "MT-CO2"
[85] "PFN1" "RPS26" "HLA-C" "RPL24" "RPS11" "MT-ND4"
[91] "MT-CYB" "RPS10" "EEF1B2" "RPS21" "COX4I1" "ARHGDIB"
[97] "RPL38" "CFL1" "H3F3B" "MT-ND1" "RPS29" "RPL36A"
[103] "MT-ND2" "ACTG1" "PFDN5" "BTF3" "GLTSCR2" "SERF2"
[109] "LTB" "SH3BGRL3" "HNRNPA1" "JUNB" "NPM1" "RPL23"
[115] "RPL17" "GAPDH" "CD52" "SLC25A6" "PABPC1" "UBC"
[121] "CYBA" "UBB" "OAZ1" "RPL22" "RPL36AL" "FXYD5"
[127] "EEF2" "LDHB" "ATP5G2" "S100A4" "CD74" "BTG1"
[133] "ATP5E" "ATP5L" "DDX5" "MYL6" "RPL41" "HLA-E"
[139] "HINT1" "MYL12A" "MT-ATP6" "TOMM7" "EIF3K" "CORO1A"
[145] "YBX1" "COX7C" "CD37" "PTPRCAP" "VIM" "COMMD6"
[151] "S100A6" "SRP14" "ARPC3" "GMFG" "ZFAS1" "IER2"
[157] "CHCHD2" "CIRBP" "TMA7" "SNRPD2" "LIMD2" "PSME1"
[163] "EDF1" "ITM2B" "TMEM66" "DUSP1" "SRSF5" "JUN"
[169] "ARPC2" "EIF3F" "PPDPF" "PPIA" "C6orf48" "RAC2"
[175] "UQCRH" "COX6B1" "EIF3L" "SSR2" "HMGB1" "HSP90AA1"
[181] "CLIC1" "EIF4A1" "OST4" "EIF3H" "EMP3" "ARPC1B"
[187] "C19orf43" "FOS" "HNRNPA2B1" "GPSM3" "TAGLN2" "IFITM2"
[193] "EIF3E" "ATP5D" "MYL12B" "IL32" "HLA-DRA" "UQCR11"
[199] "NAP1L1" "MT-ND5" "CALM1" "HSPA8" "HCST" "MZT2B"
[205] "NDUFA4" "GYPC" "EIF4A2" "GSTP1" "UXT" "ALDOA"
[211] "APRT" "ENO1" "CD3D" "HSP90AB1" "SSR4" "ERP29"
[217] "EIF3G" "AES" "CNBP" "TXNIP" "ATP5O" "PNRC1"
[223] "CD3E" "LSP1" "RBM3" "PSMA7" "GPX1" "LAPTM5"
[229] "SNHG7" "VAMP8" "CCNI" "HMGN1" "HNRNPDL" "UBXN1"
[235] "NOSIP" "ATP6V1G1" "SUMO2" "CUTA" "SOD1" "HLA-DPB1"
[241] "ARL6IP4" "COX6C" "PCBP2" "TCEB2" "HLA-DRB1" "CD99"
[247] "SERP1" "COX5B" "VAMP2" "NDUFB11" "HIGD2A" "TPI1"
[253] "S100A10" "CD7" "GPX4" "CAPZB" "ANP32B" "SKP1"
[259] "TSC22D3" "UBL5" "ZFP36L2" "NEDD8" "SF3B5" "SLC25A3"
[265] "CALM2" "LAMTOR4" "SLC25A5" "EVL" "C11orf31" "SMDT1"
[271] "NDUFS5" "GIMAP7" "C9orf16" "ST13" "SNHG8" "NDUFA11"
[277] "ANAPC16" "AIF1" "ATP5A1" "PARK7" "LSM7" "ZFP36"
[283] "COX6A1" "COX7A2" "PSME2" "DRAP1" "LY6E" "HLA-DPA1"
[289] "PRR13" "SAP18" "TSPO" "ICAM3" "NFKBIA" "GSTK1"
[295] "PEBP1" "HNRNPA0" "EID1" "MIF" "EIF3D" "SRGN"
[301] "RPSAP58" "ATPIF1" "SRSF3" "UBE2D3" "GTF3A" "C19orf53"
[307] "CD48" "COPE" "TMEM258" "CD53" "C12orf57" "NDUFB9"
[313] "NDUFA13" "ATP6V0E1" "TRAF3IP3" "RPL39" "LDHA" "HNRNPK"
[319] "MT-ND3" "FBL" "GUK1" "JTB" "ANXA1" "NDUFB8"
[325] "UCP2" "COX5A" "TRMT112" "PSMB1" "CCDC85B" "PPP1CA"
[331] "NDUFA1" "UFC1" "UQCRB" "BRK1" "TUBA1B" "ATP5J"
[337] "UBE2D2" "COTL1" "RSL1D1" "POLR2L" "IL2RG" "RAN"
[343] "RARRES3" "YWHAB" "NKG7" "RNASET2" "TRAPPC1" "WDR83OS"
[349] "SNX3" "TPM3" "ATP6V1F" "GNLY" "EIF3M" "RHOA"
[355] "PCBP1" "KLF6" "TALDO1" "COX7A2L" "NDUFB2" "TUBA1A"
[361] "PNISR" "SERPINB1" "SCAND1" "HNRNPC" "PPIB" "SEPT7"
[367] "UQCR10" "TMBIM6" "NBEAL1" "MZT2A" "ISCU" "TSTD1"
[373] "ATP5F1" "ATP5G3" "CTSW" "ISG20" "ATP5J2" "SPCS1"
[379] "UQCRQ" "COX8A" "SNRPB" "MORF4L1" "ACAP1" "ATP5B"
[385] "ATP5H" "PRDX2" "H2AFY" "U2AF1" "TBCA" "TMEM59"
[391] "ARPC5" "BST2" "SELL" "SEC61B" "RAC1" "NHP2L1"
[397] "RABAC1" "MRPS21" "CD63" "DDT" "PGK1"
[1] "factor 2"
[1] "AIF1" "ZFAS1" "RP11-620J15.3" "PRSS57"
[5] "SERPINB1" "SNHG7" "HSP90AB1" "H2AFY"
[9] "TALDO1" "SPINK2" "CYTL1" "SOX4"
[13] "EIF3E" "TXN" "UQCRB" "GPX1"
[17] "TKT" "SNHG8" "EBPL" "STMN1"
[21] "GSTP1" "UQCRH" "LYL1" "HLA-DRA"
[25] "KIAA0125" "MT-ND3" "SNRPE" "HMGA1"
[29] "LSM7" "LST1" "HINT1" "CAT"
[33] "FCER1A" "IMPDH2" "EGFL7" "LINC00493"
[37] "SNRPD1" "NUCB2" "LSMD1" "RNF130"
[41] "C19orf77" "HIST1H4C" "APEX1" "NGFRAP1"
[45] "ANP32B" "HMGB1" "COX6B1" "RPL39"
[49] "SNRPF" "C6orf48" "TIMM13" "HSD17B11"
[53] "COX5A" "ENO1" "DDAH2" "NENF"
[57] "RPL22L1" "IGFBP7" "SH3BGRL" "LINC00152"
[61] "EPB41L4A-AS1" "SUMO2" "EIF4A1" "ESD"
[65] "NAP1L1" "PRDX6" "C14orf166" "CD164"
[69] "COMT" "EID1" "SLC25A5" "OSTC"
[73] "C14orf2" "HSPD1" "ATP5J" "LSM2"
[77] "ATP5G3" "VAMP8" "PRDX1" "RSL24D1"
[81] "TAF1D" "SHFM1" "ATP5C1" "SLC25A3"
[85] "DYNLL1" "HLA-DPB1" "PSMA4" "EIF3M"
[89] "TMEM256" "TUBA1A" "HIST1H1D" "CLIC1"
[93] "ATP5A1" "RSL1D1" "YBX3" "NDUFS4"
[97] "CD63" "SF3B14" "C7orf73" "SNX3"
[101] "NME4" "HSBP1" "SPINT2" "CST3"
[105] "RP11-354E11.2" "NDUFB4" "HSP90AA1" "HIST1H1C"
[109] "DUT"
[1] "factor 3"
[1] "RPL13" "RPL10" "RPS2" "RPL13A" "RPS6" "RPL3" "MALAT1"
[8] "B2M" "RPS3" "TMSB4X" "RPL32" "RPS4X" "RPL18A" "RPS18"
[15] "RPL11" "RPS27" "RPS14" "RPL21" "EEF1A1" "RPL19" "RPS19"
[22] "RPS12" "LTB" "RPLP2" "JUNB" "RPS3A" "RPL8" "RPL18"
[29] "RPL15" "RPS5" "RPL12" "RPL6" "TMSB10" "RPS15" "RPS9"
[36] "RPL10A" "RPL23A" "HLA-B" "RPS8" "RPS25" "RPL9" "RPL14"
[43] "RPS27A" "RPL31" "RPS15A" "RPL29" "RPS16" "RPL28" "RPL4"
[50] "RPLP1" "EEF1D" "RPL5" "RPL7" "RPL27A" "RPSA" "RPS7"
[57] "RPL34" "RPS13" "TPT1" "HLA-C" "BTG1" "ACTB" "RPS23"
[64] "GNB2L1" "RPL30" "CD3E" "CD3D" "RPL26" "CD52" "RPL36"
[71] "RPL35A" "HLA-A" "RPL35" "RPL7A" "RPLP0" "UBA52" "MT-CO1"
[78] "FTL" "FAU" "GLTSCR2" "RPS28" "RPS20" "IL32" "NOSIP"
[85] "PTMA" "RPL17" "NACA" "TMEM66" "RPS10" "IER2" "RPS26"
[92] "RPL22" "CD27" "GIMAP7" "COX4I1" "MT-CO3" "PFN1" "RPL27"
[99] "CORO1A" "EEF1B2" "FTH1" "LDHB"
[1] "factor 4"
[1] "GNLY" "NKG7" "GZMB" "GZMA" "TYROBP" "CCL5"
[7] "CST7" "FCER1G" "CLIC3" "HCST" "CTSW" "KLRB1"
[13] "FGFBP2" "IFITM2" "MALAT1" "PRF1" "CD7" "HOPX"
[19] "CYBA" "B2M" "PFN1" "PLAC8" "CD247" "HLA-C"
[25] "GZMH" "CALM1" "GZMM" "FCGR3A" "SPON2" "HLA-B"
[31] "KLRF1" "HLA-A" "MYL12A" "SRGN" "ACTB" "TMSB4X"
[37] "EFHD2" "ITGB2" "CCL4" "PTPRCAP" "IFITM1" "KLRD1"
[43] "RARRES3" "HLA-E" "CD63" "ID2" "SERF2" "RAC2"
[49] "UBB" "ATP5E" "ARPC2" "JAK1" "SNORD3B-2" "MT-CO2"
[55] "MATK" "RHOC" "POLR2L" "TMA7" "MT-ATP6" "KLRC1"
[61] "RPS27" "CFL1" "CLIC1" "C12orf75" "RPL37A" "DBI"
[67] "S100A4" "ALOX5AP" "SH3BGRL3" "SEPT7" "IL2RB"
[1] "factor 5"
[1] "S100A9" "S100A8" "LYZ" "CST3" "TYROBP" "HLA-DRB1"
[7] "S100A4" "S100A6" "CD74" "FTL" "LGALS1" "HLA-DRA"
[13] "HLA-DRB5" "FTH1" "LST1" "AIF1" "FCER1G" "FCN1"
[19] "HLA-DPB1" "SAT1" "PSAP" "CYBA" "GPX1" "TYMP"
[25] "S100A11" "TSPO" "GSTP1" "CTSS" "HLA-DPA1" "FOS"
[31] "COTL1" "PYCARD" "HLA-DQB1" "CFD" "S100A10" "ATP5E"
[37] "MYL6" "HLA-DQA1" "LGALS2" "CEBPD" "OAZ1" "CD14"
[43] "FCGRT" "NEAT1" "TMEM176B" "KLF6" "LINC00936" "GRN"
[49] "NPC2" "HLA-DMA" "CFP" "LAMTOR4" "SERF2" "ARPC1B"
[55] "RAC1" "SPI1" "ANXA2"
[1] "factor 6"
character(0)
[1] "factor 7"
[1] "IL32" "S100A4" "ACTB" "SH3BGRL3" "PFN1" "LTB"
[7] "HLA-A" "CD52" "S100A10" "CD3D" "B2M" "VIM"
[13] "HLA-C" "CORO1A" "JUNB" "ACTG1" "HLA-B" "UBC"
[19] "S100A6" "CD3E" "CFL1" "GAPDH" "COTL1" "AES"
[25] "GSTK1" "ARPC1B" "ARHGDIB" "EMP3" "PTPRCAP" "TMSB4X"
[31] "CD99" "IER2" "CALM1" "FXYD5" "ANXA2" "CD2"
[37] "AQP3" "EVL" "IL2RG" "LCK" "CRIP1" "LGALS1"
[43] "HLA-E" "MYL12A" "HSPA8" "UCP2" "FTH1" "ISG20"
[49] "LAT" "CD27" "RAC2" "CAPZB" "S1PR4" "MYL6"
[55] "DOK2" "PPDPF" "TRAF3IP3" "SIT1" "CORO1B" "PKM"
[61] "GIMAP7" "LSP1" "ITM2B" "LDHB" "S100A11" "LY6E"
[67] "OAZ1" "ARPC2" "PPP1CA"
[1] "factor 8"
[1] "CD74" "HLA-DRA" "HLA-DRB1" "HLA-DPB1" "CD79A" "HLA-DPA1"
[7] "CD79B" "HLA-DRB5" "CD37" "HLA-DQA1" "MS4A1" "HLA-DQA2"
[13] "HLA-DQB1" "LTB" "CYBA" "TCL1A" "IGLL5" "HLA-DMA"
[19] "CD52" "RPS11" "HLA-DMB" "MALAT1" "NCF1" "LY86"
[25] "LINC00926" "VPREB3" "ARPC3" "OAZ1" "MT-CO1" "FCER2"
[31] "BANK1" "HVCN1" "MT-CO3"
[1] "factor 9"
[1] "CD8B" "RP11-291B21.2" "S100B" "RPS29"
[5] "HCST" "CD8A" "RPL36A" "RPS21"
[9] "RPL38" "RPS28" "CD7" "CD3D"
[13] "RPL37A" "RPL37" "RPL34" "RGS10"
[17] "MT-CO2" "RPL41" "NOSIP" "CARS"
[21] "MT-ND2" "CTSW" "RPL27" "RPS26"
[25] "RPS24" "GZMM" "RPL23" "RPL22"
[29] "RPS10"
[1] "factor 10"
[1] "SPINK2" "KIAA0125" "CD74" "HOPX" "LST1" "PRSS1"
[7] "IGJ" "HLA-DRA" "AIF1" "ZFAS1" "SNHG7" "ITM2C"
[13] "GSTP1" "TSC22D1" "ACY3" "PRSS3" "GPX1" "HLA-DPB1"
[19] "HOXA9" "C9orf89" "CALM2" "DNTT" "GNG11" "SOX4"
[25] "HLA-DPA1" "ATP5E" "MZB1" "ATP5L"
[1] "factor 11"
[1] "BTG1" "GIMAP7" "TMEM66" "LDHB" "DDX5" "PABPC1"
[7] "SELL" "NOSIP" "CD3E" "JUNB" "CCR7" "CD7"
[13] "CD27" "LEF1" "RPL4" "LTB" "GYPC" "LIMD2"
[19] "HSPA8" "TXNIP" "GPSM3" "EEF1A1" "EEF2" "TRAF3IP3"
[25] "PIK3IP1" "CNBP" "AES" "GLTSCR2" "ARHGDIB" "EEF1D"
[1] "factor 12"
[1] "GZMK" "CCL5" "IL32" "DUSP1" "GZMA" "NKG7" "JUN" "DUSP2" "LYAR"
[1] "factor 13"
[1] "S100A8" "S100A9" "FTL" "TMSB4X" "RPLP1" "TMSB10" "S100A4" "RPS14"
[9] "RPS9" "FTH1" "RPS2" "RPL13" "S100A6" "RPL13A" "MT-CO1" "FAU"
[17] "TYROBP" "RPS28" "HLA-B" "COX4I1" "RPL34"
[1] "factor 14"
[1] "TPSAB1" "LMO4" "S100A6" "APOC1" "CD63"
[1] "factor 15"
character(0)
[1] "factor 16"
[1] "CLC"
[1] "factor 17"
[1] "MT-ND2" "MT-CO2" "RPL37A" "RPL34" "RPL37" "RPL38" "RPS24"
[8] "RPS21" "RPS28" "MT-ND4" "MT-ATP6" "RPS29" "MT-CYB" "RPL27"
[15] "RPL26" "RPL35A" "RPS27A" "RPLP2" "RPS23" "RPS27" "RPL36"
[22] "MT-CO3" "RPS15A" "RPL36A" "RPL35" "RPS20" "RPS26" "RPL31"
[29] "RPLP1" "TOMM7" "MT-ND1" "RPL27A" "RPL30" "RPS12" "FAU"
[36] "RPL28" "RPL24" "RPS11" "RPL23A" "RPL23" "RPS15" "RPS19"
[43] "UBA52"
[1] "factor 18"
[1] "ZNF683" "CCL5" I tried backfitting but it gave a memory error. Setting extrapolate=FALSE fixes this (apparently extrapolation makes a copy of some big things so uses more memory).
fit2 = flash_backfit(fit1, extrapolate=FALSE)Backfitting 18 factors (tolerance: 3.10e+01)...
Difference between iterations is within 1.0e+06...
Difference between iterations is within 1.0e+05...
Difference between iterations is within 1.0e+04...
Difference between iterations is within 1.0e+03...
Difference between iterations is within 1.0e+02...
Wrapping up...
Done.saveRDS(fit2,file='../output/fit2.nn.pbmc.purified.rds')Same idea: plot the results using Eric’s code
FF_log1p = fit2$L_pm
FF_log1p <- scale(FF_log1p, center = FALSE, scale = apply(FF_log1p, 2, max))
colnames(FF_log1p) <- paste0("k", 1:ncol(FF_log1p))
FF_log1p <- FF_log1p[cell.idx, ]
log1p_tib <- make.heatmap.tib(FF_log1p)
heatmap.tib = log1p_tib
tib <- heatmap.tib %>%
group_by(Cell.type, Cell.idx) %>%
summarize()`summarise()` has grouped output by 'Cell.type'. You can override using the
`.groups` argument.cell_type_breaks <- c(1, which(tib$Cell.type[-1] != tib$Cell.type[-nrow(tib)]))
label_pos <- cell_type_breaks / 2 + c(cell_type_breaks[-1], nrow(tib)) / 2
plt <- ggplot(heatmap.tib, aes(x = Factor, y = -Cell.idx, fill = Loading)) +
geom_tile() +
scale_fill_gradient(low = "white", high = "firebrick") +
labs(y = "") +
scale_y_continuous(breaks = -label_pos,
minor_breaks = NULL,
labels = levels(cell.type)) +
scale_x_continuous(breaks = seq(0, 30, 5)) +
theme_minimal() +
geom_hline(yintercept = -cell_type_breaks, size = 0.1) +
theme(legend.position = "none",
strip.text = element_text(size = 16))
plt
List driving genes:
for(k in 1:18){
print(paste0("factor ",k))
key = fit2$F_pm[,k]>1
vals = fit2$F_pm[key,k]
print(genes$symbol[key][order(vals,decreasing =TRUE)])
}[1] "factor 1"
[1] "RPS12" "RPS18" "RPL13" "RPS27" "RPL32" "RPL13A"
[7] "RPLP2" "RPS14" "RPL34" "MALAT1" "RPS2" "RPS19"
[13] "RPLP1" "RPS6" "RPL10" "RPS15A" "RPL31" "RPS27A"
[19] "RPL21" "RPL11" "RPS3A" "RPS23" "RPS3" "RPS4X"
[25] "RPS15" "RPL23A" "RPL35A" "RPL27A" "RPL18A" "RPL3"
[31] "RPL7" "RPL28" "RPL19" "RPL26" "RPL36" "RPL12"
[37] "RPL9" "RPL30" "RPS8" "RPS25" "RPL18" "RPL35"
[43] "RPS16" "RPS13" "RPL10A" "RPS28" "RPS9" "RPS20"
[49] "RPS7" "RPL15" "RPL29" "RPS5" "FAU" "RPL37A"
[55] "TPT1" "RPL6" "RPL37" "RPL27" "RPL14" "RPL8"
[61] "RPL7A" "RPL5" "RPS24" "UBA52" "B2M" "RPSA"
[67] "TMSB4X" "RPS26" "TMSB10" "RPL24" "RPS11" "GNB2L1"
[73] "MT-CO2" "RPLP0" "NACA" "RPS21" "RPL38" "RPL4"
[79] "MT-CO3" "EEF1A1" "RPL36A" "MT-CO1" "EEF1B2" "RPS10"
[85] "PTMA" "MT-ND2" "MT-ND4" "RPS29" "MT-CYB" "RPL23"
[91] "EEF1D" "FTL" "PFDN5" "FTH1" "EIF1" "MT-ND1"
[97] "COX4I1" "RPL22" "RPL36AL" "TOMM7" "GLTSCR2" "HLA-B"
[103] "BTF3" "RPL17" "RPL41" "NPM1" "HNRNPA1" "SERF2"
[109] "ATP5L" "COX7C" "HLA-A" "COMMD6" "MT-ATP6" "ATP5E"
[115] "HINT1" "ATP5G2" "PABPC1" "SLC25A6" "FXYD5" "H3F3B"
[121] "EEF2" "SNRPD2" "ACTB" "EIF3K" "HLA-C" "ZFAS1"
[127] "TMA7" "UBB" "PFN1" "OST4" "C6orf48" "EDF1"
[133] "MT-ND5" "UXT" "EIF3E" "CFL1" "CIRBP" "CD52"
[139] "GAPDH" "OAZ1" "SRSF5" "UQCRH" "MYL12A" "CD37"
[145] "MZT2B" "MYL6" "UQCR11" "SH3BGRL3" "EIF3F" "SSR4"
[151] "YBX1" "ARHGDIB" "COX6B1" "NAP1L1" "LDHB" "CYBA"
[157] "ACTG1" "SRP14" "EIF3H" "EIF3L" "IFITM2" "GMFG"
[163] "SSR2" "VIM" "JUN" "S100A6" "BTG1" "CHCHD2"
[169] "UBC" "ATP5O" "ATP5D" "NDUFA4" "ITM2B" "PNRC1"
[175] "SERP1" "APRT" "FOS" "HSP90AB1" "HSP90AA1" "SMDT1"
[181] "IER2" "ERP29" "JUNB" "HLA-E" "PSME1" "PPDPF"
[187] "C19orf43" "DDX5" "COX6C" "SNHG8" "DUSP1" "RPL39"
[193] "EIF3G" "C12orf57" "TCEB2" "HMGB1" "NDUFB11" "ARPC3"
[199] "CUTA" "EIF4A2" "TXNIP" "HIGD2A" "TMEM66" "GPSM3"
[205] "PPIA" "SKP1" "HMGN1" "LAMTOR4" "NDUFS5" "VAMP2"
[211] "UBL5" "CCNI" "COX7A2" "SNHG7" "COX5B" "UBXN1"
[217] "FBL" "GPX4" "MIF" "TMEM258" "S100A4" "ATP6V1G1"
[1] "factor 2"
[1] "CD74" "ZFAS1" "GAPDH" "AIF1"
[5] "HLA-DRA" "SERPINB1" "SNHG7" "ACTG1"
[9] "HINT1" "HSP90AB1" "SPINK2" "EIF3E"
[13] "PRSS57" "NPM1" "ARHGDIB" "LDHB"
[17] "H2AFY" "BTF3" "RP11-620J15.3" "TALDO1"
[21] "H3F3B" "RPS24" "ENO1" "EIF4A1"
[25] "CLIC1" "TKT" "ATP5G2" "UQCRH"
[29] "HLA-DPB1" "VIM" "GSTP1" "SNHG8"
[33] "NAP1L1" "GNB2L1" "HNRNPA1" "C6orf48"
[37] "EEF2" "TAGLN2" "UBB" "HMGB1"
[41] "PABPC1" "UQCRB" "GMFG" "ANXA1"
[45] "EBPL" "TXN" "HLA-DPA1" "GPX1"
[49] "FOS" "EEF1B2" "MT-CO1" "NUCB2"
[53] "VAMP8" "RPLP0" "EIF3L" "COX6B1"
[57] "NACA" "RPL5" "LSM7" "MT-ND3"
[61] "RPL7A" "FTL" "SUMO2" "PRDX1"
[65] "PTMA" "MT-ATP6" "RPL15" "MT-CO3"
[69] "ANP32B" "EGFL7" "SLC25A3" "FTH1"
[73] "RPL23" "KIAA0125" "YBX1" "RSL1D1"
[77] "MT-ND4" "DUSP1" "COX7C" "HMGA1"
[81] "RPL29" "IMPDH2" "C19orf77" "SELL"
[85] "LYL1" "RPS21" "TUBA1A" "SOX4"
[89] "ARPC3" "RPL24" "CHCHD2" "HLA-DRB1"
[93] "SLC25A5" "ATP5A1" "MT-CYB" "ATP5L"
[97] "HSP90AA1" "SNRPE" "EIF1" "HSD17B11"
[101] "STMN1" "EID1" "BST2" "APEX1"
[105] "RPL38" "EIF3H" "RPL37A" "SRP14"
[109] "SNX3" "RBM3" "ZFP36L2" "RPL39"
[113] "SLC25A6" "CYTL1" "ALDOA" "RPS4X"
[117] "PRDX6" "SRSF5" "GYPC" "LINC00493"
[121] "CCNI" "NGFRAP1" "CAT" "UXT"
[125] "MT-ND1" "FXYD5" "COX5A" "EIF3D"
[129] "ST13" "ATP5O" "CD37" "RPS8"
[133] "PCBP2" "HIST1H4C" "EIF3M" "CD164"
[137] "EPB41L4A-AS1" "ATP5C1" "ARPC2" "RPL36A"
[141] "LST1" "C14orf166" "RPS11" "SNRPD1"
[145] "RPL10A" "NDUFA4" "RPL37" "CD99"
[149] "COMMD6" "PSME1" "RPS7" "SH3BGRL"
[153] "RPL12" "EIF3F" "MT-ND5" "SRSF3"
[157] "SNRPD2" "CRHBP" "ATP5G3" "CIRBP"
[161] "UFC1" "MDK" "ICAM3" "HLA-A"
[165] "LSM2" "LDHA" "RPS23" "RAC2"
[169] "ACTB" "TUBA1B" "PLAC8" "DYNLL1"
[173] "IGFBP7" "RPL4" "AVP" "ATP5J"
[177] "RPS5" "PNRC1" "MT-ND2" "OAZ1"
[181] "RSL24D1" "TIMM13" "SKP1" "TPI1"
[185] "PPIA" "RPL14" "RPS2" "HNRNPA2B1"
[189] "SH3BGRL3" "MZT2B" "PNISR" "ATP5B"
[193] "HSPB1" "RPS9" "TAF1D" "CCT4"
[197] "EIF3K" "FBL" "RPL3" "RPL26"
[201] "RPSA" "MYL12B" "UBC" "MT-CO2"
[205] "CFL1" "TPT1" "SRGN" "RBMX"
[209] "DDAH2" "HIST1H1C" "PFN1" "PEBP1"
[213] "RPL6" "CCT8" "COX6C" "RPS13"
[217] "SOD1" "SNRPF" "ATP6V1F" "PARK7"
[221] "SYPL1" "EIF4A2" "RPL35A" "NDUFS5"
[225] "HNRNPC" "FKBP1A" "MYL6" "ATP5D"
[229] "RPLP1" "SERPINB6" "ESD" "PSMB1"
[233] "SERP1" "HSPD1" "ARPC1B" "RPS3"
[237] "YBX3" "RPS3A" "RPS29" "HIST1H1D"
[241] "ID1" "NDUFB4" "HMGN1" "NENF"
[245] "TMEM59" "GDI2" "RPL8" "RPL35"
[249] "OSTC" "COX5B" "COX7A2" "TBCA"
[253] "MRPS21"
[1] "factor 3"
[1] "MALAT1" "RPL13" "RPL10" "RPS2" "B2M" "RPL13A"
[7] "TMSB4X" "RPS6" "RPL3" "RPS3" "RPS4X" "RPS18"
[13] "RPL18A" "RPL32" "RPL11" "RPS27" "RPS14" "RPS19"
[19] "RPL19" "HLA-B" "RPL21" "TMSB10" "RPLP2" "RPL15"
[25] "RPS12" "RPL8" "RPS15" "RPL12" "RPS3A" "ACTB"
[31] "EEF1A1" "RPL18" "RPLP1" "RPL6" "RPS9" "HLA-A"
[37] "FTL" "RPL23A" "RPS8" "RPL28" "RPS27A" "MT-CO1"
[43] "HLA-C" "RPL10A" "RPL29" "RPL14" "RPS7" "RPS5"
[49] "RPS15A" "RPL31" "RPL9" "RPL27A" "GNB2L1" "RPL26"
[55] "FTH1" "JUNB" "RPS23" "EEF1D" "RPL5" "RPS16"
[61] "RPL7" "RPS25" "PTMA" "TPT1" "RPL7A" "RPL35A"
[67] "RPL30" "RPSA" "RPL4" "RPS13" "PFN1" "RPL35"
[73] "FAU" "EIF1" "RPL36" "RPL34" "LTB" "RPLP0"
[79] "MT-CO3" "UBA52" "RPS28" "NACA" "UBC" "BTG1"
[85] "SH3BGRL3" "CD52" "RPS20" "ARHGDIB" "CFL1" "GLTSCR2"
[91] "RPS26" "H3F3B" "COX4I1" "IL32" "IER2" "JUN"
[97] "CYBA"
[1] "factor 4"
[1] "GNLY" "NKG7" "MALAT1" "B2M" "TYROBP" "ACTB"
[7] "PFN1" "TMSB4X" "GZMB" "GZMA" "HLA-B" "HLA-A"
[13] "CCL5" "HLA-C" "HCST" "CST7" "FCER1G" "CYBA"
[19] "IFITM2" "CTSW" "CLIC3" "CD7" "TMSB10" "MT-CO1"
[25] "KLRB1" "FGFBP2" "CFL1" "RPS27" "HOPX" "MYL12A"
[31] "PTPRCAP" "CALM1" "ACTG1" "PLAC8" "PRF1" "UBB"
[37] "MT-CO2" "EIF1" "ARHGDIB" "SERF2" "SH3BGRL3" "HLA-E"
[43] "S100A4" "SRGN" "RAC2" "H3F3B" "ARPC2" "CD247"
[49] "GZMM" "RPL37A" "MT-CO3" "ATP5E" "CLIC1" "PTMA"
[55] "CORO1A" "MYL6" "RPL37" "MT-ATP6" "GZMH" "ITGB2"
[61] "DDX5" "RPS28" "SPON2" "FCGR3A" "IFITM1" "LSP1"
[67] "RPS26" "RARRES3" "UBC" "TMA7" "KLRF1" "CD63"
[73] "RPS21" "RPS29" "RPL10" "FTL" "EMP3" "GSTP1"
[79] "CD99" "RPS24" "RPS15A" "PPIA" "MYL12B" "ID2"
[85] "EFHD2" "PSME1" "RPS27A" "ARPC3" "GAPDH" "RPLP2"
[91] "MT-CYB" "POLR2L" "RPL26" "CD53" "RPL23A" "MT-ND4"
[97] "EIF3G" "CCL4" "DUSP1" "SEPT7" "RPL27A" "RPL28"
[103] "FAU" "TPT1" "UQCR11" "RPL36AL" "RPLP1" "JAK1"
[109] "HSP90AA1" "DBI" "SRP14" "RPL38" "KLRD1" "BTG1"
[115] "RPL27" "UBA52" "RPL21" "MT-ND2" "TCEB2" "RPS19"
[121] "ANXA1" "RPL31" "HMGB1" "CHCHD2" "TXNIP" "NDUFB2"
[127] "RPL35" "PPP1CA" "HNRNPA2B1" "IL2RG" "OAZ1" "MATK"
[133] "ITM2B" "UBL5" "RHOC" "PTPRC" "SNORD3B-2" "GIMAP7"
[139] "PSMB9" "GMFG"
[1] "factor 5"
[1] "CST3" "HLA-DRA" "CD74" "LYZ" "HLA-DPB1" "HLA-DRB1"
[7] "HLA-DPA1" "HLA-DRB5" "HLA-DQA1" "LGALS1" "CYBA" "FCER1G"
[13] "TYROBP" "ACTB" "S100A10" "COTL1" "VIM" "HLA-DQB1"
[19] "GPX1" "FTH1" "GSTP1" "S100A4" "HLA-DQA2" "ARPC1B"
[25] "S100A6" "HLA-DMA" "PFN1" "MYL6" "CFL1" "LSP1"
[31] "AIF1" "ACTG1" "SH3BGRL3" "LST1" "PYCARD" "OAZ1"
[37] "FCGRT" "ARPC3" "SRGN" "GAPDH" "EIF4A1" "CALM2"
[43] "ARPC2" "FOS" "ANXA2" "S100A11" "TMSB4X" "RAC1"
[49] "SERF2" "FTL" "HLA-DMB" "ATP5E" "VAMP8" "SPI1"
[55] "TMSB10" "GRN" "CPVL" "CORO1A" "PSAP" "SLC25A6"
[61] "SAT1" "ZFP36" "AP2S1" "TYMP" "CTSS" "NPC2"
[67] "HLA-B" "PSME2" "PRELID1" "SLC25A5" "RNASET2" "CLIC1"
[73] "HLA-C" "PGLS" "ATP6V0B" "TAGLN2" "MT-CO1" "TPI1"
[79] "TUBA1B" "YBX1" "RNH1" "CSTB" "PPIA" "EIF1"
[85] "AMICA1" "PARK7" "B2M"
[1] "factor 6"
[1] "TUBA1B"
[1] "factor 7"
[1] "S100A4" "IL32" "ACTB" "PFN1" "SH3BGRL3" "LTB"
[7] "HLA-A" "B2M" "CD52" "TMSB4X" "HLA-C" "HLA-B"
[13] "S100A6" "GAPDH" "S100A10" "ACTG1" "VIM" "CFL1"
[19] "TMSB10" "EMP3" "ARPC1B" "CD3D" "PTPRCAP" "UBC"
[25] "ARHGDIB" "CORO1A" "JUNB" "MYL6" "FTH1" "CD99"
[31] "CYBA" "FXYD5" "MYL12A" "LGALS1" "EIF1" "COTL1"
[37] "CALM1" "CLIC1" "CRIP1" "GSTK1" "OAZ1" "ARPC2"
[43] "MT-CO1" "TAGLN2" "RAC2" "HLA-E" "IER2" "DUSP1"
[49] "H3F3B" "AES" "LSP1" "CD3E" "PSME1" "SERF2"
[55] "LDHB" "PPDPF" "ARPC3" "PSMA7" "CAPZB" "GMFG"
[61] "HSPA8" "YBX1" "ANXA2" "IL2RG" "MYL12B"
[1] "factor 8"
[1] "CD74" "HLA-DRA" "HLA-DRB1" "HLA-DPB1" "HLA-DPA1" "CD79A"
[7] "CD79B" "HLA-DRB5" "LTB" "CD37" "HLA-DQA1" "MALAT1"
[13] "CD52" "CYBA" "HLA-DQA2" "MT-CO1" "MS4A1" "HLA-DQB1"
[19] "PTPRCAP" "OAZ1" "ARPC3" "MT-CO3" "RPL18A" "TMSB4X"
[25] "HLA-B" "FTL" "ACTB" "LIMD2" "RPL13A" "RPS11"
[31] "HLA-C" "HLA-DMA" "RPL8" "TCL1A" "RPS2" "RPLP1"
[37] "RPS5" "RPL13" "PTMA" "HLA-A" "RPL15" "GNB2L1"
[43] "UBC" "ARHGDIB" "IGLL5" "EIF1" "LAPTM5" "CORO1A"
[49] "FAU" "RPL12" "RPL10" "TMSB10" "RPL7A" "RPL29"
[55] "RPL18" "HLA-DMB" "RPL19" "SLC25A6" "RPS23" "RPS8"
[61] "FTH1" "RPS19" "TSC22D3" "CLIC1" "BTG1" "LSP1"
[67] "EEF1A1" "NCF1" "RPSA" "MT-CO2" "RPL23A" "RPS18"
[73] "RPL11" "CD53" "RPS9" "YBX1" "RAC2" "SNX3"
[79] "LY86" "ARPC2" "UBB" "POLD4" "RPS7" "LINC00926"
[85] "ISG20" "RPLP2" "CFL1" "RPL27A" "VPREB3" "B2M"
[91] "RPS15" "DDX5" "PLAC8" "PFN1" "H3F3B"
[1] "factor 9"
[1] "CD8B" "ACTB" "CD3D" "LTB"
[5] "JUNB" "CD3E" "HLA-C" "PFN1"
[9] "HLA-B" "HCST" "CD7" "ARHGDIB"
[13] "CD52" "TMSB10" "HLA-A" "CORO1A"
[17] "NOSIP" "TMSB4X" "LDHB" "BTG1"
[21] "B2M" "IL32" "PTPRCAP" "CFL1"
[25] "GIMAP7" "CD27" "TMEM66" "ACTG1"
[29] "RGS10" "RP11-291B21.2" "GYPC" "LIMD2"
[33] "RAC2" "S100B" "CTSW"
[1] "factor 10"
[1] "CD74" "SPINK2" "HLA-DRA" "KIAA0125" "AIF1" "ZFAS1"
[7] "ACTG1" "LST1" "GSTP1" "SNHG7" "HOPX" "GPX1"
[13] "MALAT1" "HLA-DPB1" "H3F3B" "ENO1" "CALM2" "PRSS1"
[19] "RPS24" "ATP5L" "ATP5E" "HLA-DPA1" "ITM2C" "GAPDH"
[25] "SOX4" "LSP1" "HCST" "IGJ" "EIF1" "ARPC3"
[31] "CIRBP" "SRP14" "CD99" "HLA-DRB1" "FOS" "PTMA"
[37] "GNB2L1" "FTH1" "NDUFA4" "TSC22D1" "ACY3" "BTF3"
[43] "CLIC1" "ACTB" "EIF3E" "ATP5G2" "MT-CO1" "MT-ND4"
[49] "HLA-A" "NAP1L1" "SUMO2" "UBB" "NACA" "SRSF5"
[55] "CORO1A" "UBC" "COX7C" "LTB" "MT-ATP6"
[1] "factor 11"
[1] "LTB" "ACTB" "LDHB" "JUNB" "EEF1A1" "ARHGDIB" "RPL4"
[8] "BTG1" "PABPC1" "DDX5" "TMEM66" "CD3E" "RPL5" "CORO1A"
[15] "GIMAP7" "ACTG1" "PFN1" "GNB2L1" "NOSIP" "RPL3" "EEF1D"
[22] "LIMD2" "EEF2" "NPM1" "CFL1"
[1] "factor 12"
[1] "GZMK" "CCL5" "NKG7" "GZMA" "DUSP1" "MALAT1" "IL32" "B2M"
[9] "HLA-B" "HCST" "JUN" "BTG1" "HLA-C" "CST7" "TMSB4X" "DUSP2"
[17] "HLA-A"
[1] "factor 13"
[1] "S100A8" "S100A9" "FTL" "S100A4" "TYROBP" "FTH1"
[7] "S100A6" "TMSB4X" "TMSB10" "RPLP1" "CYBA" "LYZ"
[13] "CST3" "AIF1" "RPS14" "RPS9" "TSPO" "HLA-DRB1"
[19] "RPS2" "FCN1" "GPX1" "LGALS1" "LST1" "SAT1"
[25] "COX4I1" "SERF2" "ATP5E" "RPL13" "RPL34" "PSAP"
[31] "MT-ND1"
[1] "factor 14"
[1] "RP11-620J15.3" "SERPINB1" "HSP90AB1" "GAPDH"
[5] "S100A4" "PRSS57" "LDHB" "HMGB1"
[9] "ZFAS1" "GPX1" "FCER1A"
[1] "factor 15"
character(0)
[1] "factor 16"
[1] "S100A6" "TPSAB1" "LMO4" "CLC"
[1] "factor 17"
character(0)
[1] "factor 18"
[1] "ZNF683" "CCL5"
sessionInfo()R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.4.4 flashier_1.0.7 magrittr_2.0.3 ebnm_1.1-2 Matrix_1.6-4
[6] stringr_1.5.1 purrr_1.0.2 tidyr_1.3.0 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.12 horseshoe_0.2.0 invgamma_1.1 lattice_0.22-5
[5] rprojroot_2.0.4 digest_0.6.33 utf8_1.2.4 truncnorm_1.0-9
[9] R6_2.5.1 evaluate_0.23 highr_0.10 pillar_1.9.0
[13] rlang_1.1.2 rstudioapi_0.15.0 irlba_2.3.5.1 whisker_0.4.1
[17] jquerylib_0.1.4 rmarkdown_2.25 splines_4.2.1 Rtsne_0.17
[21] munsell_0.5.0 mixsqp_0.3-54 compiler_4.2.1 httpuv_1.6.13
[25] xfun_0.41 pkgconfig_2.0.3 SQUAREM_2021.1 htmltools_0.5.7
[29] tidyselect_1.2.0 tibble_3.2.1 workflowr_1.7.1 fansi_1.0.6
[33] crayon_1.5.2 withr_3.0.0 later_1.3.2 grid_4.2.1
[37] jsonlite_1.8.8 gtable_0.3.4 lifecycle_1.0.4 git2r_0.33.0
[41] scales_1.3.0 cli_3.6.2 stringi_1.8.3 cachem_1.0.8
[45] farver_2.1.1 fs_1.6.3 promises_1.2.1 bslib_0.6.1
[49] generics_0.1.3 vctrs_0.6.5 trust_0.1-8 tools_4.2.1
[53] glue_1.6.2 softImpute_1.4-1 parallel_4.2.1 fastmap_1.1.1
[57] yaml_2.3.8 colorspace_2.1-0 ashr_2.2-63 deconvolveR_1.2-1
[61] knitr_1.45 sass_0.4.8