Error in .local(counts, ...) : Either provide the slingshot object using the sds argument, or provide pseudotime and cell-level weights manually using pseudotime and cellWeights arguments.
chungsai opened this issue · 1 comments
Hello I am doing the vignette code by code
of here https://kstreet13.github.io/bioc2020trajectories/articles/workshopTrajectories.html
https://github.com/kstreet13/bioc2020trajectories/blob/master/vignettes/workshopTrajectories.Rmd
However, as I get to this point
set.seed(3)
icMat <- evaluateK(counts = as.matrix(assays(sce)$counts),
pseudotime = colData(sce)$slingshot$pseudotime,
cellWeights = colData(sce)$slingshot$cellWeights.V1,
conditions = factor(colData(sce)$pheno$treatment_id),
nGenes = 300,
k = 3:7)
I get error
Error in .local(counts, ...) :
Either provide the slingshot object using the sds argument, or provide pseudotime and cell-level weights manually using pseudotime and cellWeights arguments.
print(sce)
class: SingleCellExperiment
dim: 10549 9268
metadata(1): tradeSeq
assays(1): counts
rownames(10549): AP006222.2 SAMD11 ... AC011043.1 AL592183.1
rowData names(2): tradeSeq assocRes
colnames(9268): AAACATACGAATAG-1_Mock_TGFB_agregated_samples
AAACATACGCTAAC-1_Mock_TGFB_agregated_samples ...
TTTGCATGAAGTAG-4_Mock_TGFB_agregated_samples TTTGCATGCTGAGT-4_Mock_TGFB_agregated_samples
colData names(6): pheno tradeSeq ... slingPseudotime_1 slingPseudotime_1
reducedDimNames(1): UMAP
mainExpName: NULL
altExpNames(0):
print(SlingshotDataSet(sce)
- )
class: SlingshotDataSet
Samples Dimensions
9268 2
lineages: 1
Lineage1: inner outer
curves: 1
Curve1: Length: 21.008 Samples: 9268
And I cannot move forward
Session info ──────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.2 (2023-10-31)
os macOS Ventura 13.0
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Toronto
date 2024-02-21
rstudio 2023.12.1+402 Ocean Storm (desktop)
pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
abind * 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
annotate * 1.80.0 2023-10-26 [1] Bioconductor
AnnotationDbi * 1.64.1 2023-11-02 [1] Bioconductor
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.3.0)
AUCell * 1.24.0 2023-10-24 [1] Bioconductor
babelgene 22.9 2022-09-29 [1] CRAN (R 4.3.0)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.3.0)
V beachmat 2.18.0 2024-02-17 [1] Bioconductor 3.18 (R 4.3.2) (on disk 2.18.1)
beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.3.0)
Biobase * 2.62.0 2023-10-26 [1] Bioconductor
bioc2020trajectories 0.0.0.93 2024-02-22 [1] Github (kstreet13/bioc2020trajectories@d0a386f)
BiocFileCache 2.10.1 2023-10-26 [1] Bioconductor
BiocGenerics * 0.48.1 2023-11-02 [1] Bioconductor
BiocManager * 1.30.22 2023-08-08 [1] CRAN (R 4.3.0)
BiocNeighbors 1.20.2 2024-01-13 [1] Bioconductor 3.18 (R 4.3.2)
BiocParallel 1.36.0 2023-10-26 [1] Bioconductor
BiocSingular 1.18.0 2023-11-06 [1] Bioconductor
biomaRt * 2.58.2 2024-02-03 [1] Bioconductor 3.18 (R 4.3.2)
Biostrings 2.70.2 2024-01-30 [1] Bioconductor 3.18 (R 4.3.2)
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
bluster 1.12.0 2023-12-19 [1] Bioconductor 3.18 (R 4.3.2)
V boot 1.3-28.1 2024-02-19 [1] CRAN (R 4.3.1) (on disk 1.3.29)
bslib 0.6.1 2023-11-28 [1] CRAN (R 4.3.1)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
V callr 3.7.3 2024-02-19 [1] CRAN (R 4.3.1) (on disk 3.7.5)
caTools 1.18.2 2021-03-28 [1] CRAN (R 4.3.0)
celda * 1.18.1 2023-12-23 [1] Bioconductor 3.18 (R 4.3.2)
checkmate 2.3.1 2023-12-04 [1] CRAN (R 4.3.1)
class 7.3-22 2023-05-03 [1] CRAN (R 4.3.2)
classInt 0.4-10 2023-09-05 [1] CRAN (R 4.3.0)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1)
cluster 2.1.6 2023-12-01 [1] CRAN (R 4.3.1)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.2)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
combinat 0.0-8 2012-10-29 [1] CRAN (R 4.3.0)
cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.3.1)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
curl 5.2.0 2023-12-08 [1] CRAN (R 4.3.1)
data.table * 1.15.0 2024-01-30 [1] CRAN (R 4.3.1)
V DBI 1.2.1 2024-02-16 [1] CRAN (R 4.3.1) (on disk 1.2.2)
dbplyr 2.4.0 2023-10-26 [1] CRAN (R 4.3.1)
DDRTree * 0.1.5 2017-04-30 [1] CRAN (R 4.3.0)
DelayedArray * 0.28.0 2023-11-06 [1] Bioconductor
DelayedMatrixStats * 1.24.0 2023-11-06 [1] Bioconductor
deldir 2.0-2 2023-11-23 [1] CRAN (R 4.3.1)
desc 1.4.3 2023-12-10 [1] CRAN (R 4.3.1)
devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.34 2024-01-11 [1] CRAN (R 4.3.1)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.3.0)
dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.3.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.1)
dqrng 0.3.2 2023-11-29 [1] CRAN (R 4.3.1)
e1071 1.7-14 2023-12-06 [1] CRAN (R 4.3.1)
edgeR 4.0.15 2024-02-10 [1] Bioconductor 3.18 (R 4.3.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
enrichR 3.2 2023-04-14 [1] CRAN (R 4.3.0)
evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0)
fastDummies 1.7.3 2023-07-06 [1] CRAN (R 4.3.0)
fastICA 1.2-4 2023-11-27 [1] CRAN (R 4.3.1)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
fastmatch 1.1-4 2023-08-18 [1] CRAN (R 4.3.0)
fgsea * 1.28.0 2023-10-26 [1] Bioconductor
filelock 1.0.3 2023-12-11 [1] CRAN (R 4.3.1)
fitdistrplus 1.1-11 2023-04-25 [1] CRAN (R 4.3.0)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.3.0)
foreach * 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
foreign 0.8-86 2023-11-28 [1] CRAN (R 4.3.1)
Formula 1.2-5 2023-02-24 [1] CRAN (R 4.3.0)
fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0)
future 1.33.1 2023-12-22 [1] CRAN (R 4.3.1)
future.apply 1.11.1 2023-12-21 [1] CRAN (R 4.3.1)
gam * 1.22-3 2023-11-29 [1] CRAN (R 4.3.1)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
GenomeInfoDb * 1.38.6 2024-02-10 [1] Bioconductor 3.18 (R 4.3.2)
GenomeInfoDbData 1.2.11 2024-01-17 [1] Bioconductor
GenomicRanges * 1.54.1 2023-10-30 [1] Bioconductor
ggbeeswarm * 0.7.2 2023-04-29 [1] CRAN (R 4.3.0)
ggplot2 * 3.4.4 2023-10-12 [1] CRAN (R 4.3.1)
ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.3.1)
ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.3.1)
ggthemes * 5.1.0 2024-02-10 [1] CRAN (R 4.3.1)
glmGamPoi 1.14.3 2024-02-10 [1] Bioconductor 3.18 (R 4.3.2)
globals 0.16.2 2022-11-21 [1] CRAN (R 4.3.0)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1)
goftest 1.2-3 2021-10-07 [1] CRAN (R 4.3.0)
gplots * 3.1.3.1 2024-02-02 [1] CRAN (R 4.3.1)
gprofiler2 * 0.2.2 2023-06-14 [1] CRAN (R 4.3.0)
graph * 1.80.0 2023-10-26 [1] Bioconductor
gridExtra * 2.3 2017-09-09 [1] CRAN (R 4.3.0)
GSEABase * 1.64.0 2023-10-26 [1] Bioconductor
GSVA * 1.50.0 2023-11-06 [1] Bioconductor
gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0)
gtools 3.9.5 2023-11-20 [1] CRAN (R 4.3.1)
harmony * 1.2.0 2023-11-29 [1] CRAN (R 4.3.1)
V HDF5Array 1.30.0 2024-02-17 [1] Bioconductor 3.18 (R 4.3.2) (on disk 1.30.1)
Hmisc * 5.1-1 2023-09-12 [1] CRAN (R 4.3.0)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
HSMMSingleCell 1.22.0 2023-10-26 [1] Bioconductor
htmlTable 2.4.2 2023-10-29 [1] CRAN (R 4.3.1)
htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1)
httpuv 1.6.14 2024-01-26 [1] CRAN (R 4.3.1)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0)
ica 1.0-3 2022-07-08 [1] CRAN (R 4.3.0)
V igraph 2.0.1.1 2024-02-17 [1] CRAN (R 4.3.1) (on disk 2.0.2)
IRanges * 2.36.0 2023-10-26 [1] Bioconductor
irlba * 2.3.5.1 2022-10-03 [1] CRAN (R 4.3.0)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0)
jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1)
KEGGREST 1.42.0 2023-10-26 [1] Bioconductor
KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.3.2)
knitr * 1.45 2023-10-30 [1] CRAN (R 4.3.1)
labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1)
lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
leiden 0.4.3.1 2023-11-17 [1] CRAN (R 4.3.1)
leidenbase 0.1.27 2023-12-01 [1] CRAN (R 4.3.1)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1)
limma * 3.58.1 2023-11-02 [1] Bioconductor
listenv 0.9.1 2024-01-29 [1] CRAN (R 4.3.1)
lme4 1.1-35.1 2023-11-05 [1] CRAN (R 4.3.1)
lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.3.0)
locfit 1.5-9.8 2023-06-11 [1] CRAN (R 4.3.0)
lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.3.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
MASS * 7.3-60.0.1 2024-01-13 [1] CRAN (R 4.3.1)
mathjaxr 1.6-0 2022-02-28 [1] CRAN (R 4.3.0)
Matrix * 1.6-5 2024-01-11 [1] CRAN (R 4.3.1)
MatrixGenerics * 1.14.0 2023-10-26 [1] Bioconductor
matrixStats * 1.2.0 2023-12-11 [1] CRAN (R 4.3.1)
MCMCprecision 0.4.0 2019-12-05 [1] CRAN (R 4.3.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
metap 1.9 2023-10-09 [1] CRAN (R 4.3.1)
metapod 1.10.1 2023-12-23 [1] Bioconductor 3.18 (R 4.3.2)
mgcv 1.9-1 2023-12-21 [1] CRAN (R 4.3.1)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
minqa 1.2.6 2023-09-11 [1] CRAN (R 4.3.0)
mnormt 2.1.1 2022-09-26 [1] CRAN (R 4.3.0)
monocle3 * 1.3.4 2024-02-15 [1] Github (cole-trapnell-lab/monocle3@2b17745)
msigdbr * 7.5.1 2022-03-30 [1] CRAN (R 4.3.0)
multcomp 1.4-25 2023-06-20 [1] CRAN (R 4.3.0)
multtest * 2.58.0 2023-10-26 [1] Bioconductor
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
mutoss 0.1-13 2023-03-14 [1] CRAN (R 4.3.0)
mvtnorm 1.2-4 2023-11-27 [1] CRAN (R 4.3.1)
nlme 3.1-164 2023-11-27 [1] CRAN (R 4.3.1)
nloptr 2.0.3 2022-05-26 [1] CRAN (R 4.3.0)
nnet 7.3-19 2023-05-03 [1] CRAN (R 4.3.2)
numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.3.0)
openxlsx * 4.2.5.2 2023-02-06 [1] CRAN (R 4.3.0)
org.Hs.eg.db * 3.18.0 2024-02-15 [1] Bioconductor
org.Rn.eg.db * 3.18.0 2024-02-15 [1] Bioconductor
V parallelly 1.36.0 2024-02-14 [1] CRAN (R 4.3.1) (on disk 1.37.0)
patchwork 1.2.0 2024-01-08 [1] CRAN (R 4.3.1)
pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.3.0)
pbmcapply 1.5.1 2022-04-28 [1] CRAN (R 4.3.0)
pheatmap * 1.0.12 2019-01-04 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.3 2023-12-10 [1] CRAN (R 4.3.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.1)
plotly 4.10.4 2024-01-13 [1] CRAN (R 4.3.1)
plotrix 3.8-4 2023-11-10 [1] CRAN (R 4.3.1)
plyr 1.8.9 2023-10-02 [1] CRAN (R 4.3.1)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
Polychrome * 1.5.1 2022-05-03 [1] CRAN (R 4.3.0)
polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.3.1)
presto * 1.0.0 2024-02-08 [1] Github (immunogenomics/presto@31dc97f)
prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.3.1)
princurve * 2.1.6 2021-01-18 [1] CRAN (R 4.3.0)
processx 3.8.3 2023-12-10 [1] CRAN (R 4.3.1)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
progress 1.2.3 2023-12-06 [1] CRAN (R 4.3.1)
progressr 0.14.0 2023-08-10 [1] CRAN (R 4.3.0)
promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0)
proxy 0.4-27 2022-06-09 [1] CRAN (R 4.3.0)
ps 1.7.6 2024-01-18 [1] CRAN (R 4.3.1)
purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.3.0)
qqconf 1.3.2 2023-04-14 [1] CRAN (R 4.3.0)
R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0)
R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.3.1)
R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.3.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
ragg 1.2.7 2023-12-11 [1] CRAN (R 4.3.1)
RANN 2.6.1 2019-01-08 [1] CRAN (R 4.3.0)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
rbibutils 2.2.16 2023-10-25 [1] CRAN (R 4.3.1)
RColorBrewer * 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
Rcpp * 1.0.12 2024-01-09 [1] CRAN (R 4.3.1)
RcppAnnoy 0.0.22 2024-01-23 [1] CRAN (R 4.3.1)
RcppEigen 0.3.3.9.4 2023-11-02 [1] CRAN (R 4.3.1)
RcppHNSW 0.6.0 2024-02-04 [1] CRAN (R 4.3.1)
RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.3.1)
Rdpack 2.6 2023-11-08 [1] CRAN (R 4.3.1)
readr * 2.1.5 2024-01-10 [1] CRAN (R 4.3.1)
remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0)
reshape2 * 1.4.4 2020-04-09 [1] CRAN (R 4.3.0)
reticulate 1.35.0 2024-01-31 [1] CRAN (R 4.3.1)
rhdf5 2.46.1 2023-12-02 [1] Bioconductor 3.18 (R 4.3.2)
rhdf5filters 1.14.1 2023-12-16 [1] Bioconductor 3.18 (R 4.3.2)
Rhdf5lib 1.24.2 2024-02-10 [1] Bioconductor 3.18 (R 4.3.2)
RhpcBLASctl 0.23-42 2023-02-11 [1] CRAN (R 4.3.0)
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1)
rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1)
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.3.0)
rpart 4.1.23 2023-12-05 [1] CRAN (R 4.3.1)
RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.3.0)
RSQLite 2.3.5 2024-01-21 [1] CRAN (R 4.3.1)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0)
rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.3.0)
Rtsne 0.17 2023-12-07 [1] CRAN (R 4.3.1)
s2 1.1.6 2023-12-19 [1] CRAN (R 4.3.1)
S4Arrays * 1.2.0 2023-10-26 [1] Bioconductor
S4Vectors * 0.40.2 2023-11-25 [1] Bioconductor 3.18 (R 4.3.2)
sandwich 3.1-0 2023-12-11 [1] CRAN (R 4.3.1)
sass 0.4.8 2023-12-06 [1] CRAN (R 4.3.1)
ScaledMatrix 1.10.0 2023-11-06 [1] Bioconductor
scales * 1.3.0 2023-11-28 [1] CRAN (R 4.3.1)
scater * 1.30.1 2023-11-16 [1] Bioconductor
scattermore 1.2 2023-06-12 [1] CRAN (R 4.3.0)
scatterplot3d 0.3-44 2023-05-05 [1] CRAN (R 4.3.0)
scClustViz * 1.3.12 2023-11-21 [1] Github (BaderLab/scClustViz@6707c89)
SCINA * 1.2.0 2019-07-18 [1] CRAN (R 4.3.0)
scran * 1.30.2 2024-01-23 [1] Bioconductor 3.18 (R 4.3.2)
sctransform 0.4.1 2023-10-19 [1] CRAN (R 4.3.1)
scuttle * 1.12.0 2023-11-06 [1] Bioconductor
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
Seurat * 5.0.1 2023-11-17 [1] CRAN (R 4.3.1)
SeuratObject * 5.0.1 2023-11-17 [1] CRAN (R 4.3.1)
SeuratWrappers * 0.3.19 2024-02-08 [1] Github (inofechm/seurat-wrappers@73466e3)
sf 1.0-15 2023-12-18 [1] CRAN (R 4.3.1)
shiny * 1.8.0 2023-11-17 [1] CRAN (R 4.3.1)
SingleCellExperiment * 1.24.0 2023-11-06 [1] Bioconductor
slam 0.1-50 2022-01-08 [1] CRAN (R 4.3.0)
slingshot * 2.10.0 2023-10-26 [1] Bioconductor
sn 2.1.1 2023-04-04 [1] CRAN (R 4.3.0)
SoupX * 1.6.2 2022-11-01 [1] CRAN (R 4.3.0)
sp * 2.1-3 2024-01-30 [1] CRAN (R 4.3.1)
spam 2.10-0 2023-10-23 [1] CRAN (R 4.3.1)
SparseArray * 1.2.4 2024-02-10 [1] Bioconductor 3.18 (R 4.3.2)
sparseMatrixStats 1.14.0 2023-10-26 [1] Bioconductor
spatstat.data 3.0-4 2024-01-15 [1] CRAN (R 4.3.1)
spatstat.explore 3.2-6 2024-02-01 [1] CRAN (R 4.3.1)
spatstat.geom 3.2-8 2024-01-26 [1] CRAN (R 4.3.1)
spatstat.random 3.2-2 2023-11-29 [1] CRAN (R 4.3.1)
spatstat.sparse 3.0-3 2023-10-24 [1] CRAN (R 4.3.1)
spatstat.utils 3.0-4 2023-10-24 [1] CRAN (R 4.3.1)
spData 2.3.0 2023-07-06 [1] CRAN (R 4.3.0)
spdep 1.3-3 2024-02-07 [1] CRAN (R 4.3.1)
statmod 1.5.0 2023-01-06 [1] CRAN (R 4.3.0)
stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.1)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.3.1)
SummarizedExperiment * 1.32.0 2023-11-06 [1] Bioconductor
V survival 3.5-7 2024-02-14 [1] CRAN (R 4.3.1) (on disk 3.5.8)
systemfonts 1.0.5 2023-10-09 [1] CRAN (R 4.3.1)
tensor 1.5 2012-05-05 [1] CRAN (R 4.3.0)
terra 1.7-71 2024-01-31 [1] CRAN (R 4.3.1)
textshaping 0.3.7 2023-10-09 [1] CRAN (R 4.3.1)
TFisher 0.2.0 2018-03-21 [1] CRAN (R 4.3.0)
TH.data 1.1-2 2023-04-17 [1] CRAN (R 4.3.0)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.3.1)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.3.0)
timechange 0.3.0 2024-01-18 [1] CRAN (R 4.3.1)
tradeSeq * 1.16.0 2023-10-26 [1] Bioconductor
TrajectoryUtils * 1.10.1 2024-02-06 [1] Bioconductor 3.18 (R 4.3.2)
tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.3.0)
units 0.8-5 2023-11-28 [1] CRAN (R 4.3.1)
UpSetR * 1.4.0 2019-05-22 [1] CRAN (R 4.3.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
V usethis * 2.2.2 2024-02-19 [1] CRAN (R 4.3.1) (on disk 2.2.3)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1)
uwot 0.1.16 2023-06-29 [1] CRAN (R 4.3.0)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1)
VGAM * 1.1-9 2023-09-19 [1] CRAN (R 4.3.1)
vipor 0.4.7 2023-12-18 [1] CRAN (R 4.3.1)
viridis * 0.6.5 2024-01-29 [1] CRAN (R 4.3.1)
viridisLite * 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1)
wk 0.9.1 2023-11-29 [1] CRAN (R 4.3.1)
WriteXLS 6.5.0 2024-01-09 [1] CRAN (R 4.3.1)
xfun 0.42 2024-02-08 [1] CRAN (R 4.3.1)
XML * 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.3.1)
xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
XVector 0.42.0 2023-10-26 [1] Bioconductor
yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1)
zip 2.3.1 2024-01-27 [1] CRAN (R 4.3.1)
zlibbioc 1.48.0 2023-10-26 [1] Bioconductor
zoo 1.8-12 2023-04-13 [1] CRAN (R 4.3.0)
[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
V ── Loaded and on-disk version mismatch.
Hi @chungsai
The code you refer to is from a workshop from 4 years ago, and we are no longer maintaining the code of that workflow. Our apologies.