Attaching SeuratObject
Loading required package: ensembldb
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
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clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
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anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
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Loading required package: IRanges
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Loading required package: AnnotationDbi
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")'.
Possible Ensembl SSL connectivity problems detected.
Please see the 'Connection Troubleshooting' section of the biomaRt vignette
vignette('accessing_ensembl', package = 'biomaRt')Error in curl::curl_fetch_memory(url, handle = handle) :
SSL peer certificate or SSH remote key was not OK: [uswest.ensembl.org] SSL certificate problem: certificate has expired
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
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Loading required package: BSgenome
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Attaching package: 'Biostrings'
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strsplit
Loading required package: rtracklayer
Attaching package: 'dplyr'
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slice
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filter, select
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select
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combine
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intersect, setdiff, union
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intersect
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collapse, desc, intersect, setdiff, slice, union
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first, intersect, rename, setdiff, setequal, union
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combine, intersect, setdiff, union
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filter, lag
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intersect, setdiff, setequal, union
Attaching package: 'cowplot'
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align_plots
Attaching package: 'tidyr'
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expand
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smiths
corrplot 0.92 loaded
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Attaching package: 'MASS'
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area
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Attaching package: 'plotly'
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select
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export
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layout
Attaching package: 'clustifyrdata'
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downrefs, s_small, s_small3
DOSE v3.16.0 For help: https://guangchuangyu.github.io/software/DOSE
If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609
Loading required package: usethis
── Attaching core tidyverse packages ───────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ forcats 1.0.0 ✔ purrr 1.0.2
✔ lubridate 1.9.3 ✔ readr 2.1.4
── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ lubridate::%within%() masks IRanges::%within%()
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✖ plotly::slice() masks dplyr::slice(), XVector::slice(), IRanges::slice()
✖ lubridate::stamp() masks cowplot::stamp()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Attaching package: 'reshape'
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stamp
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rename
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colsplit, melt, recast
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expand, smiths
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stamp
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rename
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expand, rename
Loading required package: ggraph
Loading required package: PRROC
Loading required package: WriteXLS
Loading required package: rpart
Loading required package: rpart.plot
clusterProfiler v3.18.1 For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
Attaching package: 'clusterProfiler'
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select
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Fetching data...
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aggregating...
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Fetching data...
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aggregating...
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aggregating...
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aggregating...
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aggregating...
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aggregating...
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aggregating...
Done
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
Warning message in .Seqinfo.mergexy(x, y):
"The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)"
