Back to Books build report for BioC 3.12

BUILD report for OSCA on nebbiolo1

This page was generated on 2021-05-05 15:35:02 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the OSCA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1/2HostnameOS / ArchINSTALLBUILD
OSCA 1.0.6  (landing page)
Aaron Lun
Snapshot Date: 2021-05-05 07:00:01 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/OSCA
Branch: RELEASE_3_12
Last Commit: bb87e03
Last Changed Date: 2020-11-13 15:15:29 -0400 (Fri, 13 Nov 2020)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  

Summary

Package: OSCA
Version: 1.0.6
Command: /home/biocbuild/bbs-3.12-books/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA
StartedAt: 2021-05-05 07:30:09 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 08:40:34 -0400 (Wed, 05 May 2021)
EllapsedTime: 4225.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-books/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA
###
##############################################################################
##############################################################################


* checking for file ‘OSCA/DESCRIPTION’ ... OK
* preparing ‘OSCA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’

cd book && "/home/biocbuild/bbs-3.12-books/R/bin/R" -e "bookdown::render_book('index.Rmd')"

R version 4.0.4 (2021-02-15) -- "Lost Library Book"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> bookdown::render_book('index.Rmd')


processing file: index.Rmd

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output file: index.knit.md



processing file: introduction.Rmd

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output file: introduction.knit.md



processing file: learning-r-and-bioconductor.Rmd

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output file: learning-r-and-bioconductor.knit.md



processing file: beyond-r-basics.Rmd

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Loading required package: SummarizedExperiment
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Loading required package: GenomicRanges
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    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

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Loading required package: IRanges
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Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  :
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output file: data-infrastructure.knit.md

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 $ fig.cap: chr "UMAP plot of the retina dataset, where each point is a cell and is colored by the cluster identity."

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    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
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    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
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    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
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Welcome to Bioconductor

    Vignettes contain introductory material; view with
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    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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using temporary cache /tmp/RtmpHNCFsm/BiocFileCache
snapshotDate(): 2020-10-27
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
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    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
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    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
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    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
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    parLapplyLB, parRapply, parSapply, parSapplyLB

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    IQR, mad, sd, var, xtabs

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    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
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Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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output file: quality-control.knit.md



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Welcome to Bioconductor

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output file: normalization.knit.md

Warning messages:
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---------------------
Welcome to dendextend version 1.14.0
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
---------------------


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Genes in the gene sets NOT available in the dataset: 
	endothelial-mural: 	7 (8% of 83)
	interneurons: 	1 (1% of 118)
	oligodendrocytes: 	2 (2% of 81)
	pyramidal CA1: 	4 (3% of 125)
	pyramidal SS: 	4 (3% of 149)

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label: auc-dist (with options) 
List of 4
 $ results   : chr "hide"
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label: aucell-muraro-heat (with options) 
List of 3
 $ fig.asp : num 1
 $ fig.wide: logi TRUE
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Genes in the gene sets NOT available in the dataset: 
	Zheng_Cord_Blood_C1_Putative_Megakaryocyte_Progenitor: 	10 (10% of 98)
	Zheng_Cord_Blood_C2_Putative_Basophil_Eosinophil_Mast_cell_Progenitor: 	4 (4% of 96)
	Zheng_Cord_Blood_C3_Megakaryocyte_Erythroid_Progenitor: 	5 (5% of 100)
	Zheng_Cord_Blood_C4_Putative_Early_Erythroid_Commitment: 	5 (5% of 97)
	Zheng_Cord_Blood_C5_Similar_to_HSC_C6_Putative_Altered_Metabolic_State: 	29 (30% of 97)
	Zheng_Cord_Blood_C6_HSC_Multipotent_Progenitor: 	8 (8% of 97)
	Zheng_Cord_Blood_C7_Putative_Lymphoid_Primed_Multipotent_Progenitor_1: 	12 (13% of 95)
	Zheng_Cord_Blood_C8_Putative_Lymphoid_Primed_Multipotent_Progenitor_2: 	20 (21% of 97)
	Zheng_Cord_Blood_C9_Granulocyte_Macrophage_Progenitor: 	6 (6% of 100)
	Zheng_Cord_Blood_C10_Multilymphoid_Progenitor: 	13 (13% of 97)
	Gao_Esophagus_25W_C1_Ciliated_Epithelial_Cells: 	64 (14% of 455)
	Gao_Esophagus_25W_C2_KRT6Bpos_Secretory_Progenitor_Cells: 	10 (13% of 77)
	Gao_Esophagus_25W_C3_FGFR1Low_Epithelial_Cells: 	6 (12% of 52)
	Gao_Esophagus_25W_C4_FGFR1High_Epithelial_Cells: 	23 (11% of 208)
	Gao_Stomach_24W_C1_PROCRpos_Multipotent_Progenitor: 	1 (2% of 40)
	Gao_Stomach_24W_C2_TFF2pos_Multipotent_Progenitor: 	1 (14% of 7)
	Gao_Stomach_24W_C5_Putative_Pit_Cell_Progenitor: 	5 (9% of 55)
	Gao_Small_Intestine_24W_C2_PROCRpos_Progenitor: 	1 (5% of 22)
	Gao_Small_Intestine_24W_C3_Enterocyte_Progenitor_Subtype_1: 	2 (4% of 48)
	Gao_Small_Intestine_24W_C4_Enterocyte_Progenitor_Subtype_2: 	13 (14% of 96)
	Gao_Small_Intestine_24W_C6_Goblet_Cells: 	3 (7% of 44)
	Gao_Small_Intestine_24W_C7_Secretory_Progenitor: 	10 (20% of 51)
	Gao_Small_Intestine_24W_C9_Enteroendocrine_Cell: 	17 (28% of 60)
	Gao_Large_Intestine_24W_C1_DCLK1pos_Progenitor: 	4 (4% of 99)
	Gao_Large_Intestine_24W_C2_MKI67pos_Progenitor: 	6 (5% of 113)
	Gao_Large_Intestine_24W_C5_LGR5pos_Stem_Cell: 	6 (10% of 60)
	Gao_Large_Intestine_24W_C6_Secretory_Progenitor: 	3 (14% of 21)
	Gao_Large_Intestine_24W_C8_Goblet_Cell: 	1 (2% of 41)
	Gao_Large_Intestine_24W_C10_Enterocyte: 	7 (12% of 56)
	Gao_Large_Intestine_24W_C11_Paneth_Like_Cell: 	20 (6% of 323)
	Gao_Large_Intestine_Adult_CA_enteroendocrine_cells: 	28 (9% of 309)
	Gao_Large_Intestine_Adult_CE_OLFM4high_Stem_Cell: 	45 (12% of 362)
	Gao_Large_Intestine_Adult_CF_Goblet_Cell_Subtype_1: 	2 (9% of 23)
	Gao_Large_Intestine_Adult_CG_Goblet_Cell_Subtype_2: 	11 (20% of 55)
	Gao_Large_Intestine_Adult_CH_MKI67high_Cells: 	9 (8% of 107)
	Gao_Large_Intestine_Adult_CI_Mesenchymal_Cells: 	44 (12% of 361)
	Gao_Large_Intestine_Adult_CJ_Immune_Cells: 	40 (8% of 503)
	Zhong_PFC_Major_Types_Astrocytes: 	26 (8% of 325)
	Zhong_PFC_Major_Types_Excitatory_Neuron: 	1 (12% of 8)
	Zhong_PFC_Major_Types_Microglia: 	31 (7% of 437)
	Zhong_PFC_Major_Types_NPCs: 	9 (6% of 142)
	Zhong_PFC_Major_Types_OPC: 	7 (8% of 91)
	Zhong_PFC_C7_oRG_undergoing_Neuronal_Differentiation: 	9 (13% of 67)
	Zhong_PFC_C8_oRG_Proliferating: 	2 (3% of 62)
	Zhong_PFC_C9_oRG_Other: 	8 (10% of 83)
	Zhong_PFC_C3_Unknown_INP: 	4 (11% of 38)
	Zhong_PFC_C4_Unknown_INP: 	6 (7% of 89)
	Zhong_PFC_C5_BCL11B_CALB2_pos_INP: 	1 (5% of 22)
	Zhong_PFC_HES1_pos_C1_NPC: 	1 (17% of 6)
	Zhong_PFC_C2_Unknown_NPC: 	2 (3% of 75)
	Zhong_PFC_C1_NEUROD1_pos_Excitatory_Neuron: 	1 (4% of 26)
	Zhong_PFC_C2_SOX5_BCL11B_pos_Excitatory_Neuron: 	2 (7% of 28)
	Zhong_PFC_C6_PLXNA4_pos_Excitatory_Neuron: 	1 (14% of 7)
	Zhong_PFC_C6_DLX5_GAD1_GAD2_pos_Interneuron: 	2 (13% of 15)
	Zhong_PFC_C7_SST_LHX6_pos_Putative_Migrating_Interneuron: 	2 (14% of 14)
	Zhong_PFC_C8_Unknown_NEUROD2_pos_Interneuron: 	5 (6% of 84)
	Zhong_PFC_C1_OPC: 	17 (7% of 237)
	Zhong_PFC_C2_THY1_pos_OPC: 	1 (4% of 27)
	Zhong_PFC_C3_HOPX_pos_OPC: 	1 (12% of 8)
	Zhong_PFC_C4_PTGDS_pos_OPC: 	9 (6% of 147)
	Zhong_PFC_C1_Astrocyte: 	4 (13% of 30)
	Zhong_PFC_C2_ASCL1_pos_Astrocyte: 	2 (33% of 6)
	Zhong_PFC_C3_Astrocyte: 	36 (9% of 386)
	Zhong_PFC_C1_Microglia: 	12 (5% of 255)
	Zhong_PFC_C3_Microglia: 	36 (7% of 488)
	Fan_Embryonic_CTX_Big_Groups_Cajal_Retzius: 	47 (9% of 499)
	Fan_Embryonic_CTX_Big_Groups_Brain_Endothelial: 	21 (6% of 365)
	Fan_Embryonic_CTX_Big_Groups_Excitatory_Neuron: 	6 (13% of 47)
	Fan_Embryonic_CTX_Big_Groups_Glial: 	6 (5% of 133)
	Fan_Embryonic_CTX_Big_Groups_Brain_Immune: 	12 (8% of 148)
	Fan_Embryonic_CTX_Big_Groups_Microglia: 	23 (6% of 371)
	Fan_Embryonic_CTX_EX_1_Excitatory_Neuron: 	2 (29% of 7)
	Fan_Embryonic_CTX_EX_2_Excitatory_Neuron: 	2 (12% of 16)
	Fan_Embryonic_CTX_EX_4_Excitatory_Neuron: 	17 (10% of 162)
	Fan_Embryonic_CTX_IN_1_Interneuron: 	1 (9% of 11)
	Fan_Embryonic_CTX_IN_2_Interneuron: 	2 (29% of 7)
	Fan_Embryonic_CTX_Astrocyte_1: 	8 (10% of 79)
	Fan_Embryonic_CTX_Astrocyte_2: 	20 (13% of 153)
	Fan_Embryonic_CTX_NSC_1: 	1 (6% of 18)
	Fan_Embryonic_CTX_NSC_2: 	11 (5% of 233)
	Fan_Embryonic_CTX_Olig: 	53 (7% of 753)
	Fan_Embryonic_CTX_OPC: 	7 (13% of 55)
	Fan_Embryonic_CTX_Brain_Endothelial_1: 	30 (7% of 439)
	Fan_Embryonic_CTX_Brain_Endothelial_2: 	18 (6% of 303)
	Fan_Embryonic_CTX_Microglia_1: 	8 (5% of 154)
	Fan_Embryonic_CTX_Microglia_3: 	2 (10% of 20)
	Fan_Embryonic_CTX_Brain_Myeloid: 	12 (9% of 139)
	Fan_Embryonic_CTX_Brain_B_cell: 	14 (14% of 100)
	Fan_Embryonic_CTX_Brain_Effector_T_cell: 	19 (15% of 131)
	Fan_Embryonic_CTX_Brain_Naive_like_T_cell: 	18 (11% of 158)
	Manno_Midbrain_Neurotypes_Basal: 	12 (15% of 79)
	Manno_Midbrain_Neurotypes_hEndo: 	63 (7% of 889)
	Manno_Midbrain_Neurotypes_hPeric: 	66 (8% of 795)
	Manno_Midbrain_Neurotypes_hMgl: 	31 (5% of 576)
	Manno_Midbrain_Neurotypes_hOPC: 	36 (10% of 365)
	Manno_Midbrain_Neurotypes_hRgl2c: 	35 (11% of 326)
	Manno_Midbrain_Neurotypes_hRgl2b: 	55 (13% of 439)
	Manno_Midbrain_Neurotypes_hRgl2a: 	63 (11% of 598)
	Manno_Midbrain_Neurotypes_hRgl3: 	62 (11% of 572)
	Manno_Midbrain_Neurotypes_hRgl1: 	39 (11% of 364)
	Manno_Midbrain_Neurotypes_hProgM: 	29 (9% of 306)
	Manno_Midbrain_Neurotypes_hProgBP: 	34 (11% of 300)
	Manno_Midbrain_Neurotypes_hProgFPL: 	31 (10% of 323)
	Manno_Midbrain_Neurotypes_hProgFPM: 	35 (10% of 355)
	Manno_Midbrain_Neurotypes_hNProg: 	21 (9% of 229)
	Manno_Midbrain_Neurotypes_hNbM: 	19 (6% of 295)
	Manno_Midbrain_Neurotypes_hNbML1: 	24 (7% of 327)
	Manno_Midbrain_Neurotypes_hRN: 	19 (6% of 333)
	Manno_Midbrain_Neurotypes_hNbML5: 	35 (8% of 465)
	Manno_Midbrain_Neurotypes_hDA: 	46 (9% of 507)
	Manno_Midbrain_Neurotypes_hDA1: 	34 (6% of 585)
	Manno_Midbrain_Neurotypes_hDA2: 	37 (7% of 514)
	Manno_Midbrain_Neurotypes_hNbGaba: 	58 (8% of 702)
	Manno_Midbrain_Neurotypes_hGaba: 	93 (8% of 1106)
	Manno_Midbrain_Neurotypes_hSert: 	41 (9% of 451)
	Manno_Midbrain_Neurotypes_hOMTN: 	26 (7% of 387)
	Hay_Bone_Marrow_CD34_pos_CLP: 	27 (32% of 85)
	Hay_Bone_Marrow_CD34_pos_Eo_B_Mast: 	23 (32% of 73)
	Hay_Bone_Marrow_CD34_pos_ERP: 	23 (33% of 69)
	Hay_Bone_Marrow_CD34_pos_ERP_Early: 	18 (25% of 73)
	Hay_Bone_Marrow_CD34_pos_Gran: 	44 (32% of 138)
	Hay_Bone_Marrow_CD34_pos_HSC: 	162 (27% of 607)
	Hay_Bone_Marrow_CD34_pos_HSC_cycle: 	17 (37% of 46)
	Hay_Bone_Marrow_CD34_pos_LMPP: 	46 (40% of 115)
	Hay_Bone_Marrow_CD34_pos_Lymphoid_UNK: 	18 (35% of 51)
	Hay_Bone_Marrow_CD34_pos_MDP_1: 	20 (53% of 38)
	Hay_Bone_Marrow_CD34_pos_MDP_2: 	11 (35% of 31)
	Hay_Bone_Marrow_CD34_pos_MEP: 	20 (43% of 46)
	Hay_Bone_Marrow_CD34_pos_MKP: 	39 (20% of 193)
	Hay_Bone_Marrow_CD34_pos_MultiLin: 	47 (27% of 174)
	Hay_Bone_Marrow_CD34_pos_pre_B: 	134 (26% of 519)
	Hay_Bone_Marrow_CD34_pos_pre_B_cycling: 	44 (44% of 99)
	Hay_Bone_Marrow_CD34_pos_pre_PC: 	190 (28% of 679)
	Hay_Bone_Marrow_CD34_pos_pre_T: 	15 (47% of 32)
	Hay_Bone_Marrow_CD8_T_cell: 	155 (28% of 551)
	Hay_Bone_Marrow_Dendritic_Cell: 	175 (24% of 721)
	Hay_Bone_Marrow_Early_Erythroblast: 	76 (12% of 648)
	Hay_Bone_Marrow_Eosinophil: 	109 (24% of 456)
	Hay_Bone_Marrow_Follicular_B_cell: 	223 (31% of 710)
	Hay_Bone_Marrow_Granulocytic_UNK: 	28 (32% of 87)
	Hay_Bone_Marrow_Immature_Neutrophil: 	159 (18% of 876)
	Hay_Bone_Marrow_Monocyte: 	164 (24% of 686)
	Hay_Bone_Marrow_Naive_T_cell: 	386 (25% of 1561)
	Hay_Bone_Marrow_Neutrophil: 	233 (17% of 1356)
	Hay_Bone_Marrow_NK_cells: 	246 (13% of 1842)
	Hay_Bone_Marrow_Plasma_Cell: 	247 (49% of 509)
	Hay_Bone_Marrow_Platelet: 	104 (22% of 481)
	Hay_Bone_Marrow_Pre_Dendritic: 	31 (38% of 82)
	Hay_Bone_Marrow_Pro_B: 	179 (16% of 1086)
	Hay_Bone_Marrow_Stromal: 	291 (17% of 1754)
	Aizarani_Liver_C1_NK_NKT_cells_1: 	26 (17% of 157)
	Aizarani_Liver_C2_Kupffer_Cells_1: 	7 (4% of 200)
	Aizarani_Liver_C3_NK_NKT_cells_2: 	21 (13% of 162)
	Aizarani_Liver_C4_EPCAM_pos_bile_duct_cells_1: 	10 (5% of 191)
	Aizarani_Liver_C5_NK_NKT_cells_3: 	25 (20% of 126)
	Aizarani_Liver_C6_Kupffer_Cells_2: 	14 (6% of 228)
	Aizarani_Liver_C7_EPCAM_pos_bile_duct_cells_2: 	11 (5% of 219)
	Aizarani_Liver_C8_Resident_B_cells_1: 	5 (14% of 35)
	Aizarani_Liver_C9_LSECs_1: 	22 (7% of 305)
	Aizarani_Liver_C10_MVECs_1: 	16 (6% of 270)
	Aizarani_Liver_C11_Hepatocytes_1: 	24 (8% of 298)
	Aizarani_Liver_C12_NK_NKT_cells_4: 	10 (20% of 49)
	Aizarani_Liver_C13_LSECs_2: 	24 (8% of 283)
	Aizarani_Liver_C14_Hepatocytes_2: 	21 (9% of 226)
	Aizarani_Liver_C17_Hepatocytes_3: 	8 (8% of 102)
	Aizarani_Liver_C18_NK_NKT_cells_5: 	6 (5% of 121)
	Aizarani_Liver_C20_LSECs_3: 	21 (7% of 296)
	Aizarani_Liver_C21_Stellate_cells_1: 	6 (3% of 195)
	Aizarani_Liver_C22_Resident_B_cells_2: 	5 (15% of 33)
	Aizarani_Liver_C23_Kupffer_Cells_3: 	14 (6% of 221)
	Aizarani_Liver_C24_EPCAM_pos_bile_duct_cells_3: 	7 (4% of 185)
	Aizarani_Liver_C25_Kupffer_Cells_4: 	7 (4% of 174)
	Aizarani_Liver_C28_NK_NKT_cells_6: 	10 (10% of 99)
	Aizarani_Liver_C29_MVECs_2: 	17 (5% of 314)
	Aizarani_Liver_C30_Hepatocytes_4: 	53 (12% of 445)
	Aizarani_Liver_C31_Kupffer_Cells_5: 	8 (7% of 120)
	Aizarani_Liver_C32_MVECs_3: 	3 (2% of 125)
	Aizarani_Liver_C33_Stellate_cells_2: 	5 (4% of 126)
	Aizarani_Liver_C34_MHC_II_pos_B_cells: 	13 (10% of 134)
	Aizarani_Liver_C38_Resident_B_cells_3: 	4 (17% of 23)
	Aizarani_Liver_C39_EPCAM_pos_bile_duct_cells_4: 	5 (3% of 184)
	Menon_Fetal_Kidney_0_Cap_Mesenchyme_Cells: 	9 (10% of 90)
	Menon_Fetal_Kidney_1_Embryonic_Red_Blood_Cells: 	35 (28% of 126)
	Menon_Fetal_Kidney_2_Nephron_Progenitor_Cells: 	5 (11% of 44)
	Menon_Fetal_Kidney_3_Stromal_Cells: 	3 (4% of 81)
	Menon_Fetal_Kidney_4_Podocytes: 	12 (6% of 206)
	Menon_Fetal_Kidney_5_Proximal_Tubule_Cells: 	15 (13% of 112)
	Menon_Fetal_Kidney_6_Collecting_Duct_Cells: 	4 (4% of 94)
	Menon_Fetal_Kidney_7_Loopof_Henle_Cells_Distal: 	49 (18% of 275)
	Menon_Fetal_Kidney_8_Connecting_Tubule_Cells: 	33 (12% of 267)
	Menon_Fetal_Kidney_9_Endothelial_Cells: 	7 (7% of 102)
	Menon_Fetal_Kidney_10_Immune_Cells: 	6 (7% of 83)
	Lake_Adult_Kidney_C1_Epithelial_Cells_unassigned: 	3 (10% of 30)
	Lake_Adult_Kidney_C2_Podocytes: 	11 (5% of 212)
	Lake_Adult_Kidney_C3_Proximal_Tubule_Epithelial_Cells_S1_S2: 	26 (12% of 221)
	Lake_Adult_Kidney_C4_Proximal_Tubule_Epithelial_Cells_S2: 	15 (9% of 176)
	Lake_Adult_Kidney_C5_Proximal_Tubule_Epithelial_Cells_Stress_Inflam: 	49 (12% of 417)
	Lake_Adult_Kidney_C6_Proximal_Tubule_Epithelial_Cells_Fibrinogen_pos_S3: 	7 (4% of 181)
	Lake_Adult_Kidney_C7_Proximal_Tubule_Epithelial_Cells_S3: 	5 (4% of 135)
	Lake_Adult_Kidney_C8_Decending_thin_Limb: 	12 (4% of 278)
	Lake_Adult_Kidney_C9_Thin_ascending_limb: 	12 (4% of 268)
	Lake_Adult_Kidney_C10_Thin_ascending_limb: 	22 (6% of 353)
	Lake_Adult_Kidney_C11_Thin_ascending_limb: 	8 (5% of 169)
	Lake_Adult_Kidney_C12_Thick_Ascending_Limb: 	33 (9% of 380)
	Lake_Adult_Kidney_C13_Thick_Ascending_Limb: 	14 (11% of 131)
	Lake_Adult_Kidney_C14_Distal_Convoluted_Tubule: 	13 (6% of 208)
	Lake_Adult_Kidney_C15_Connecting_Tubule: 	10 (6% of 171)
	Lake_Adult_Kidney_C16_Collecting_system_Principal_Cells_cortex: 	10 (7% of 141)
	Lake_Adult_Kidney_C17_Collecting_system_PCs_Stressed_Dissoc_Subset: 	9 (4% of 240)
	Lake_Adult_Kidney_C18_Collecting_Duct_Principal_Cells_medulla: 	18 (6% of 322)
	Lake_Adult_Kidney_C19_Collecting_Duct_Intercalated_Cells_Type_A_medulla: 	23 (7% of 326)
	Lake_Adult_Kidney_C20_Collecting_Duct_Intercalated_Cells_Type_A_cortex: 	14 (9% of 152)
	Lake_Adult_Kidney_C21_Collecting_Duct_Intercalated_Cells_Type_B: 	6 (6% of 103)
	Lake_Adult_Kidney_C22_Endothelial_Cells_glomerular_capillaries: 	4 (3% of 137)
	Lake_Adult_Kidney_C23_Endothelial_Cells_AVR: 	8 (6% of 126)
	Lake_Adult_Kidney_C24_Endothelial_Cells_AEA_and_DVR: 	4 (3% of 152)
	Lake_Adult_Kidney_C25_Endothelial_Cells_unassigned: 	1 (3% of 38)
	Lake_Adult_Kidney_C26_Mesangial_Cells: 	8 (5% of 177)
	Lake_Adult_Kidney_C27_Vascular_Smooth_Muscle_Cells_and_pericytes: 	7 (5% of 155)
	Lake_Adult_Kidney_C28_Interstitium: 	5 (6% of 86)
	Lake_Adult_Kidney_C29_Unknown_Novel_PT_CFH_pos_Subpopulation_S2: 	8 (9% of 86)
	Hu_Fetal_Retina_Amacrine: 	4 (6% of 64)
	Hu_Fetal_Retina_Bipolar: 	13 (15% of 86)
	Hu_Fetal_Retina_Blood: 	38 (13% of 282)
	Hu_Fetal_Retina_Fibroblast: 	24 (6% of 385)
	Hu_Fetal_Retina_Horizontal: 	6 (15% of 40)
	Hu_Fetal_Retina_Microglia: 	24 (6% of 382)
	Hu_Fetal_Retina_Muller: 	1 (2% of 42)
	Hu_Fetal_Retina_Photoreceptor: 	13 (18% of 71)
	Hu_Fetal_Retina_RGC: 	24 (5% of 443)
	Hu_Fetal_Retina_RPC: 	8 (7% of 107)
	Hu_Fetal_Retina_RPE: 	39 (13% of 292)
	Muraro_Pancreas_Alpha_Cell: 	39 (7% of 566)
	Muraro_Pancreas_Beta_Cell: 	50 (5% of 948)
	Muraro_Pancreas_Delta_Cell: 	14 (6% of 249)
	Muraro_Pancreas_Pancreatic_Polypeptide_Cell: 	9 (6% of 155)
	Muraro_Pancreas_Epsilon_Cell: 	1 (2% of 44)
	Muraro_Pancreas_Ductal_Cell: 	58 (5% of 1277)
	Muraro_Pancreas_Acinar_Cell: 	20 (3% of 731)
	Muraro_Pancreas_Mesenchymal_Stromal_Cell: 	25 (4% of 680)
	Muraro_Pancreas_Endothelial_Cell: 	18 (5% of 362)
Genes in the gene sets NOT available in the dataset: 
	Muraro_Pancreas_Alpha_Cell: 	39 (7% of 566)
	Muraro_Pancreas_Beta_Cell: 	50 (5% of 948)
	Muraro_Pancreas_Delta_Cell: 	14 (6% of 249)
	Muraro_Pancreas_Pancreatic_Polypeptide_Cell: 	9 (6% of 155)
	Muraro_Pancreas_Epsilon_Cell: 	1 (2% of 44)
	Muraro_Pancreas_Ductal_Cell: 	58 (5% of 1277)
	Muraro_Pancreas_Acinar_Cell: 	20 (3% of 731)
	Muraro_Pancreas_Mesenchymal_Stromal_Cell: 	25 (4% of 680)
	Muraro_Pancreas_Endothelial_Cell: 	18 (5% of 362)

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output file: cell-annotation.knit.md



processing file: data-integration.Rmd

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