Based on rocker/geospatial:4.0.2. Includes tools for single cell RNA seq/ATAC analysis
1.6K
Includes the following single-omics analysis tools (version details below):
| Package Name |
| ArchR |
| CellChat |
| CoGAPS |
| clusterProfiler |
| InferCNV |
| Monocle3 |
| NicheNetR |
| scran |
| scater |
| SingleR |
| Seurat |
Complete list of installed R packages and versions (all Python dependencies for all packages also installed):
| Package Name | Version |
| abind | 1.4-5 |
| annotate | 1.68.0 |
| AnnotationDbi | 1.52.0 |
| ape | 5.5 |
| ArchR | 1.0.1 |
| argparse | 2.0.1 |
| arrow | 1.0.1 |
| askpass | 1.1 |
| assertthat | 0.2.1 |
| backports | 1.1.10 |
| base64enc | 0.1-3 |
| batchelor | 1.6.3 |
| BBmisc | 1.11 |
| beachmat | 2.6.4 |
| beeswarm | 0.2.3 |
| BH | 1.75.0-0 |
| Biobase | 2.50.0 |
| BiocGenerics | 0.36.1 |
| BiocManager | 1.30.15 |
| BiocNeighbors | 1.8.2 |
| BiocParallel | 1.24.1 |
| BiocSingular | 1.6.0 |
| BiocVersion | 3.12.0 |
| biocViews | 1.58.1 |
| Biostrings | 2.58.0 |
| bit | 4.0.4 |
| bit64 | 4.0.5 |
| bitops | 1.0-7 |
| blob | 1.2.1 |
| blogdown | 0.2 |
| bluster | 1.0.0 |
| bookdown | 0.2 |
| brew | 1.0-6 |
| brio | 1.1.2 |
| broom | 0.7.1 |
| BSgenome | 1.58.0 |
| BSgenome.Hsapiens.UCSC.hg38 | 1.4.3 |
| bslib | 0.2.5.1 |
| cachem | 1.0.5 |
| Cairo | 1.5-12.2 |
| callr | 3.7.0 |
| car | 3.0-10 |
| carData | 3.0-4 |
| caret | 6.0-86 |
| caTools | 1.18.2 |
| cellranger | 1.1.0 |
| checkmate | 2.0.0 |
| chromVAR | 1.12.0 |
| circlize | 0.4.10 |
| classInt | 0.4-3 |
| cli | 2.5.0 |
| clipr | 0.7.0 |
| clue | 0.3-57 |
| clusterProfiler | 3.18.1 |
| CNEr | 1.26.0 |
| coda | 0.19-4 |
| CoGAPS | 3.10.0 |
| coin | 1.3-1 |
| colorspace | 2.0-1 |
| combinat | 0.0-8 |
| commonmark | 1.7 |
| ComplexHeatmap | 2.6.2 |
| conquer | 1.0.2 |
| corrplot | 0.84 |
| covr | 3.5.1 |
| cowplot | 1.1.1 |
| cpp11 | 0.2.7 |
| crayon | 1.4.1 |
| credentials | 1.3.0 |
| crosstalk | 1.1.1 |
| curl | 4.3.1 |
| data.table | 1.14.0 |
| DBI | 1.1.1 |
| dbplyr | 1.4.4 |
| DDRTree | 0.1.5 |
| DelayedArray | 0.16.3 |
| DelayedMatrixStats | 1.12.3 |
| deldir | 0.2-10 |
| densityClust | 0.3 |
| desc | 1.3.0 |
| DESeq2 | 1.30.1 |
| devtools | 2.3.2 |
| DiagrammeR | 1.0.6.1 |
| DiceKriging | 1.5.6 |
| dichromat | 2.0-0 |
| diffobj | 0.3.4 |
| digest | 0.6.27 |
| DirichletMultinomial | 1.32.0 |
| DO.db | 2.9 |
| docopt | 0.7.1 |
| doParallel | 1.0.15 |
| DOSE | 3.16.0 |
| downloader | 0.4 |
| dplyr | 1.0.6 |
| dqrng | 0.3.0 |
| DT | 0.15 |
| dtplyr | 1.0.1 |
| e1071 | 1.7-3 |
| edgeR | 3.32.1 |
| ellipsis | 0.3.2 |
| emoa | 0.5-0.1 |
| enrichplot | 1.10.2 |
| enrichR | 3 |
| evaluate | 0.14 |
| expm | 0.999-5 |
| fansi | 0.5.0 |
| farver | 2.1.0 |
| fastcluster | 1.1.25 |
| fastICA | 1.2-2 |
| fastmap | 1.1.0 |
| fastmatch | 1.1-0 |
| fdrtool | 1.2.15 |
| fgsea | 1.16.0 |
| findpython | 1.0.5 |
| fitdistrplus | 1.1-3 |
| FNN | 1.1.3 |
| forcats | 0.5.0 |
| foreach | 1.5.0 |
| formatR | 1.1 |
| Formula | 1.2-3 |
| fs | 1.5.0 |
| fst | 0.9.4 |
| furrr | 0.1.0 |
| futile.logger | 1.4.3 |
| futile.options | 1.0.1 |
| future | 1.21.0 |
| future.apply | 1.7.0 |
| gdalUtils | 2.0.3.2 |
| gdata | 2.18.0 |
| gdtools | 0.2.2 |
| genefilter | 1.72.1 |
| geneplotter | 1.68.0 |
| generics | 0.1.0 |
| GenomeInfoDb | 1.26.7 |
| GenomeInfoDbData | 1.2.4 |
| GenomicAlignments | 1.26.0 |
| GenomicRanges | 1.42.0 |
| geometry | 0.4.5 |
| geoR | 1.8-1 |
| geosphere | 1.5-10 |
| gert | 0.3 |
| GetoptLong | 1.0.3 |
| ggbeeswarm | 0.6.0 |
| ggforce | 0.3.2 |
| ggplot2 | 3.3.3 |
| ggpubr | 0.4.0 |
| ggraph | 2.0.3 |
| ggrepel | 0.9.1 |
| ggridges | 0.5.3 |
| ggsci | 2.9 |
| ggsignif | 0.6.0 |
| gh | 1.1.0 |
| git2r | 0.27.1 |
| GlobalOptions | 0.1.2 |
| globals | 0.14.0 |
| glue | 1.4.2 |
| gmodels | 2.18.1 |
| GO.db | 3.12.1 |
| goftest | 1.2-2 |
| GOSemSim | 2.16.1 |
| gower | 0.2.2 |
| gplots | 3.1.1 |
| graph | 1.68.0 |
| graphlayouts | 0.7.0 |
| gridExtra | 2.3 |
| grr | 0.9.5 |
| gstat | 2.0-6 |
| gtable | 0.3.0 |
| gtools | 3.8.2 |
| harmony | 1 |
| haven | 2.3.1 |
| HDF5Array | 1.18.1 |
| hdf5r | 1.3.3 |
| hexbin | 1.28.1 |
| HiddenMarkov | 1.8-11 |
| highr | 0.8 |
| Hmisc | 4.4-1 |
| hms | 1.1.0 |
| HSMMSingleCell | 1.10.0 |
| htmlTable | 2.1.0 |
| htmltools | 0.5.1.1 |
| htmlwidgets | 1.5.3 |
| httpuv | 1.6.1 |
| httr | 1.4.2 |
| ica | 1.0-2 |
| igraph | 1.2.6 |
| infercnv | 1.7.2 |
| influenceR | 0.1.0 |
| ini | 0.3.1 |
| intervals | 0.15.2 |
| ipred | 0.9-9 |
| IRanges | 2.24.1 |
| irlba | 2.3.3 |
| isoband | 0.2.4 |
| iterators | 1.0.12 |
| jpeg | 0.1-8.1 |
| jquerylib | 0.1.4 |
| jsonlite | 1.7.2 |
| KEGGREST | 1.30.1 |
| kernlab | 0.9-29 |
| knitr | 1.3 |
| labeling | 0.4.2 |
| Lahman | 8.0-0 |
| lambda.r | 1.2.4 |
| later | 1.2.0 |
| latticeExtra | 0.6-29 |
| lava | 1.6.8 |
| lazyeval | 0.2.2 |
| leafem | 0.1.3 |
| leaflet | 2.0.3 |
| leaflet.providers | 1.9.0 |
| leafpop | 0.0.6 |
| leafsync | 0.1.0 |
| LearnBayes | 2.15.1 |
| leiden | 0.3.8 |
| leidenbase | 0.1.3 |
| lhs | 1.1.1 |
| libcoin | 1.0-6 |
| lidR | 3.0.3 |
| lifecycle | 1.0.0 |
| limma | 3.46.0 |
| linprog | 0.9-2 |
| listenv | 0.8.0 |
| littler | 0.3.11 |
| lme4 | 1.1-23 |
| lmtest | 0.9-38 |
| locfit | 1.5-9.4 |
| lpSolve | 5.6.15 |
| lubridate | 1.7.9 |
| lwgeom | 0.2-5 |
| magic | 1.5-9 |
| magrittr | 2.0.1 |
| manipulateWidget | 0.10.1 |
| mapdata | 2.3.0 |
| maps | 3.3.0 |
| maptools | 1.0-2 |
| mapview | 2.9.0 |
| markdown | 1.1 |
| MAST | 1.16.0 |
| mathjaxr | 1.4-0 |
| Matrix | 1.3-3 |
| Matrix.utils | 0.9.8 |
| MatrixGenerics | 1.2.1 |
| MatrixModels | 0.5-0 |
| matrixStats | 0.58.0 |
| mco | 1.0-15.1 |
| memoise | 2.0.0 |
| metap | 1.4 |
| mime | 0.1 |
| miniUI | 0.1.1.1 |
| minqa | 1.2.4 |
| misc3d | 0.9-0 |
| mixtools | 1.2.0 |
| mlr | 2.18.0 |
| mlrMBO | 1.1.4 |
| mnormt | 2.0.2 |
| modeldata | 0.0.2 |
| ModelMetrics | 1.2.2.2 |
| modelr | 0.1.8 |
| modeltools | 0.2-23 |
| monocle | 2.18.0 |
| monocle3 | 1.0.0 |
| motifmatchr | 1.12.0 |
| multcomp | 1.4-17 |
| multtest | 2.46.0 |
| munsell | 0.5.0 |
| mutoss | 0.1-12 |
| mvtnorm | 1.1-1 |
| nabor | 0.5.0 |
| ncdf4 | 1.17 |
| ncmeta | 0.3.0 |
| nichenetr | 1.0.0 |
| nloptr | 1.2.2.2 |
| numDeriv | 2016.8-1.1 |
| nycflights13 | 1.0.1 |
| openssl | 1.4.4 |
| openxlsx | 4.2.2 |
| org.Hs.eg.db | 3.12.0 |
| packrat | 0.5.0 |
| parallelly | 1.25.0 |
| parallelMap | 1.5.0 |
| ParamHelpers | 1.14 |
| patchwork | 1.1.1 |
| pbapply | 1.4-3 |
| pbkrtest | 0.4-8.6 |
| pbmcapply | 1.5.0 |
| pheatmap | 1.0.12 |
| phyclust | 0.1-29 |
| pillar | 1.6.1 |
| pkgbuild | 1.1.0 |
| pkgconfig | 2.0.3 |
| pkgload | 1.2.1 |
| plogr | 0.2.0 |
| plot3D | 1.3 |
| plotly | 4.9.3 |
| plotrix | 3.8-1 |
| plyr | 1.8.6 |
| png | 0.1-7 |
| polyclip | 1.10-0 |
| polynom | 1.4-0 |
| poweRlaw | 0.70.6 |
| pracma | 2.2.9 |
| praise | 1.0.0 |
| presto | 1.0.0 |
| prettyunits | 1.1.1 |
| pROC | 1.16.2 |
| processx | 3.5.2 |
| prodlim | 2019.11.13 |
| progress | 1.2.2 |
| proj4 | 1.0-10 |
| promises | 1.2.0.1 |
| proxy | 0.4-25 |
| ps | 1.6.0 |
| pscl | 1.5.5 |
| purrr | 0.3.4 |
| qlcMatrix | 0.9.7 |
| quantreg | 5.85 |
| qvalue | 2.22.0 |
| R.methodsS3 | 1.8.1 |
| R.oo | 1.24.0 |
| R.utils | 2.10.1 |
| R6 | 2.5.0 |
| RandomFields | 3.3.8 |
| RandomFieldsUtils | 0.5.3 |
| randomForest | 4.6-14 |
| RANN | 2.6.1 |
| rappdirs | 0.3.3 |
| raster | 3.3-13 |
| RBGL | 1.66.0 |
| rbibutils | 2.1.1 |
| rcmdcheck | 1.3.3 |
| RColorBrewer | 1.1-2 |
| Rcpp | 1.0.6 |
| RcppAnnoy | 0.0.18 |
| RcppArmadillo | 0.10.5.0.0 |
| RcppEigen | 0.3.3.9.1 |
| RcppGSL | 0.3.8 |
| RcppHNSW | 0.3.0 |
| RcppProgress | 0.4.2 |
| RcppZiggurat | 0.1.6 |
| RCSF | 1.0.2 |
| RCurl | 1.98-1.3 |
| Rdpack | 2.1.1 |
| readr | 1.4.0 |
| readxl | 1.3.1 |
| recipes | 0.1.13 |
| redland | 1.0.17-12 |
| rematch | 1.0.1 |
| rematch2 | 2.1.2 |
| remotes | 2.2.0 |
| reprex | 0.3.0 |
| reshape | 0.8.8 |
| reshape2 | 1.4.4 |
| ResidualMatrix | 1.0.0 |
| reticulate | 1.2 |
| rex | 1.2.0 |
| Rfast | 2.0.3 |
| Rfast2 | 0.0.9 |
| rgdal | 1.5-16 |
| rgeos | 0.5-5 |
| rgl | 0.100.54 |
| rhandsontable | 0.3.7 |
| rhdf5 | 2.34.0 |
| rhdf5filters | 1.2.1 |
| Rhdf5lib | 1.12.1 |
| RhpcBLASctl | 0.20-137 |
| Rhtslib | 1.22.0 |
| rio | 0.5.16 |
| rjags | 44296 |
| rJava | 0.9-13 |
| rjson | 0.2.20 |
| RJSONIO | 1.3-1.4 |
| rlang | 0.4.11 |
| rlas | 1.3.6 |
| RMariaDB | 1.0.10 |
| rmarkdown | 2.4 |
| rmdshower | 2.1.1 |
| RNetCDF | 2.4-2 |
| ROCR | 1.0-11 |
| roxygen2 | 7.1.1 |
| RPostgres | 1.2.1 |
| rprojroot | 2.0.2 |
| rsample | 0.0.8 |
| Rsamtools | 2.6.0 |
| rsconnect | 0.8.16 |
| RSpectra | 0.16-0 |
| RSQLite | 2.2.7 |
| rstatix | 0.6.0 |
| rstudioapi | 0.13 |
| rsvd | 1.0.5 |
| rticles | 0.16 |
| rtracklayer | 1.50.0 |
| Rtsne | 0.15 |
| RUnit | 0.4.32 |
| rvcheck | 0.1.8 |
| rversions | 2.0.2 |
| rvest | 0.3.6 |
| S4Vectors | 0.28.1 |
| sandwich | 3.0-1 |
| sass | 0.4.0 |
| satellite | 1.0.2 |
| scales | 1.1.1 |
| scater | 1.18.6 |
| scattermore | 0.7 |
| scatterpie | 0.1.5 |
| scran | 1.18.7 |
| sctransform | 0.3.2 |
| scuttle | 1.0.4 |
| segmented | 1.3-4 |
| selectr | 0.4-2 |
| seqLogo | 1.56.0 |
| servr | 0.19 |
| sessioninfo | 1.1.1 |
| Seurat | 4.0.0 |
| SeuratObject | 4.0.1 |
| sf | 0.9-6 |
| shadowtext | 0.0.7 |
| shape | 1.4.5 |
| shiny | 1.6.0 |
| shinythemes | 1.1.2 |
| SingleCellExperiment | 1.12.0 |
| SingleR | 1.4.1 |
| sitmo | 2.0.1 |
| slam | 0.1-48 |
| slider | 0.1.5 |
| smoof | 1.6.0.2 |
| sn | 2.0.0 |
| snow | 0.4-3 |
| sourcetools | 0.1.7 |
| sp | 1.4-2 |
| spacetime | 1.2-3 |
| SparseM | 1.81 |
| sparseMatrixStats | 1.2.1 |
| sparsesvd | 0.2 |
| spatialreg | 1.1-5 |
| spatstat | 1.64-1 |
| spatstat.core | 2.1-2 |
| spatstat.data | 2.1-0 |
| spatstat.geom | 2.1-0 |
| spatstat.linnet | 2.1-1 |
| spatstat.sparse | 2.0-0 |
| spatstat.utils | 2.1-0 |
| spData | 0.3.8 |
| spdep | 1.1-5 |
| speedglm | 0.3-2 |
| splancs | 2.01-40 |
| SQUAREM | 2020.4 |
| stars | 0.4-3 |
| statmod | 1.4.34 |
| stringi | 1.6.2 |
| stringr | 1.4.0 |
| SummarizedExperiment | 1.20.0 |
| svglite | 1.2.3.2 |
| sys | 3.4 |
| systemfonts | 0.3.2 |
| tensor | 1.5 |
| testit | 0.12 |
| testthat | 3.0.2 |
| TFBSTools | 1.28.0 |
| TFisher | 0.2.0 |
| TFMPvalue | 0.0.8 |
| TH.data | 1.0-10 |
| tibble | 3.1.2 |
| tidygraph | 1.2.0 |
| tidync | 0.2.4 |
| tidyr | 1.1.3 |
| tidyselect | 1.1.1 |
| tidyverse | 1.3.0 |
| timeDate | 3043.102 |
| tinytex | 0.26 |
| tmap | 3.2 |
| tmaptools | 3.1 |
| tmvnsim | 1.0-2 |
| tufte | 0.7 |
| tweenr | 1.0.1 |
| units | 0.6-7 |
| usethis | 1.6.3 |
| utf8 | 1.2.1 |
| uuid | 0.1-4 |
| uwot | 0.1.10 |
| vctrs | 0.3.8 |
| VGAM | 1.1-5 |
| vipor | 0.4.5 |
| viridis | 0.6.1 |
| viridisLite | 0.4.0 |
| visNetwork | 2.0.9 |
| vroom | 1.3.2 |
| waldo | 0.2.5 |
| warp | 0.1.0 |
| webshot | 0.5.2 |
| whisker | 0.4 |
| whoami | 1.3.0 |
| widgetframe | 0.3.1 |
| withr | 2.4.2 |
| xaringan | 0.17 |
| xfun | 0.18 |
| XML | 3.99-0.6 |
| xml2 | 1.3.2 |
| xopen | 1.0.0 |
| xtable | 1.8-4 |
| xts | 0.12.1 |
| XVector | 0.30.0 |
| yaml | 2.2.1 |
| zip | 2.1.1 |
| zlibbioc | 1.36.0 |
| zoo | 1.8-9 |
| base | 4.0.2 |
| boot | 1.3-25 |
| class | 7.3-17 |
| cluster | 2.1.0 |
| codetools | 0.2-16 |
| compiler | 4.0.2 |
| datasets | 4.0.2 |
| foreign | 0.8-80 |
| graphics | 4.0.2 |
| grDevices | 4.0.2 |
| grid | 4.0.2 |
| KernSmooth | 2.23-17 |
| lattice | 0.20-41 |
| MASS | 7.3-53 |
| Matrix | 1.2-18 |
| methods | 4.0.2 |
| mgcv | 1.8-33 |
| nlme | 3.1-149 |
| nnet | 7.3-14 |
| parallel | 4.0.2 |
| rpart | 4.1-15 |
| spatial | 7.3-12 |
| splines | 4.0.2 |
| stats | 4.0.2 |
| stats4 | 4.0.2 |
| survival | 3.2-7 |
| tcltk | 4.0.2 |
| tools | 4.0.2 |
| utils | 4.0.2 |
Changelog:
v2: add nichenetr and dependencies
v3: add cifs-utils and smbclient
v4: add SingleR
v5: add scran
v6: add clusterProfiler, org.Hs.eg.db, and scater. Install infercnv and dependencies - was previously installed. Install CellChat python dependencies - were not previously installed.
Content type
Image
Digest
sha256:a53eb875f…
Size
4.2 GB
Last updated
almost 4 years ago
docker pull bhuvic/singlecell:v10