This is the installation instruction for all the deconvolution programs used in the benchmarking.
We suggest to install all the programs in a conda environment. The R programs can be classifed into THREE categories: from source codes, from conda, from bioconductor and from github.
# DSA
wget https://github.com/zhandong/DSA/raw/master/Package/version_1.0/DSA_1.0.tar.gz
R CMD INSTALL DSA_1.0.tar.gz
# glmnet
conda install -c r r-glmnet
# deconrnaseq
conda install -c bioconda bioconductor-deconrnaseq
# ADAPTS dependent
conda install -c conda-forge r-foreign
conda install -c conda-forge r-rmisc
conda install -c conda-forge libcurl
# CAMTHC # this package is not used in the pipeline, instead debCAM is used
conda install -c r r-rjava
conda install -c conda-forge r-pcapp
conda install -c conda-forge r-dmwr
# CDSeq
conda install -c conda-forge r-slam
# Seurat
conda install -c conda-forge r-seuratdisk
conda install -c conda-forge r-seurat
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("impute")
BiocManager::install("GO.db")
BiocManager::install("Rhtslib")
packages <- c("devtools", "BiocManager","data.table","ggplot2","tidyverse",
"Matrix","matrixStats",
"gtools",'stringi','future','rlang','multcomp','Rtsne','irlba','ROCR',
"foreach","doMC","doSNOW", #for parallelism
"Seurat","sctransform", #sc-specific normalization
"nnls","FARDEEP","MASS","glmnet","ComICS","dtangle") #bulk deconvolution methods
for (i in packages){ install.packages(i, character.only = TRUE)}
packages3 = c('debCAM','limma','edgeR','DESeq2','pcaMethods','BiocParallel','preprocessCore','scater','SingleCellExperiment','Linnorm','DeconRNASeq','multtest','GSEABase','annotate','genefilter','preprocessCore','graph','MAST','Biobase') #last two are required by DWLS and MuSiC, respectively.
for (i in packages3){ BiocManager::install(i, character.only = TRUE)}
# Dependencies for CellMix: 'NMF', 'csSAM', 'GSEABase', 'annotate', 'genefilter', 'preprocessCore', 'limSolve', 'corpcor', 'graph', 'BiocInstaller'
packages2 = c('NMF','csSAM','limSolve','corpcor','pkgmaker', 'NMF', 'csSAM', 'registry', 'stringr', 'GSEABase', 'Biobase', 'BiocGenerics', 'annotate', 'matrixStats', 'genefilter', 'AnnotationDbi', 'RSQLite', 'DBI', 'preprocessCore', 'limSolve', 'quadprog', 'corpcor', 'xtable', 'gtools', 'beeswarm', 'graph', 'BiocInstaller', 'bibtex', 'digest', 'ggplot2', 'plyr')
for (i in packages2){ install.packages(i, character.only = TRUE)}
install.packages('remotes')
devtools::install_github("LTLA/BiocNeighbors")
devtools::install_github("GfellerLab/EPIC", build_vignettes=TRUE) #requires knitr
devtools::install_github("xuranw/MuSiC")
devtools::install_github("meichendong/SCDC")
devtools::install_github("rosedu1/deconvSeq")
devtools::install_github("cozygene/bisque")
devtools::install_github("dviraran/[email protected]")
devtools::install_github("jingshuw/descend")
install.packages("scBio")
devtools::install_github("amitfrish/scBio")
BiocManager::install("EpiDISH")
devtools::install_bitbucket("yuanlab/dwls") # this package is not used in the pipeline, instead the /DWLS.R is used
devtools::install_github("Danko-Lab/TED/TED")
devtools::install_github("chichaumiau/CellMix")
devtools::install_github("Lululuella/CAMTHC") # this package is not used in the pipeline
devtools::install_github("kkang7/CDSeq_R_Package")
devtools::install_github('shenorrlab/bseqsc')
the functions for the methods below can be found in the irrespective files in this repository: TIMER : /TIMER.R more info about the package at http://cistrome.org/TIMER/ DWLS : /DWLS.R more info about the package at https://github.com/dtsoucas/DWLS
CIBERSORT The source code for CIBERSORT can be asked from the authors at https://cibersort.stanford.edu/download.php #bseqsc method is also dependent on CIBERSORT
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)
Matrix products: default
BLAS/LAPACK: /nfs/leia/research/ma/chichau/bin/anaconda3/lib/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 compiler parallel stats graphics grDevices
[8] utils datasets methods base
other attached packages:
[1] BisqueRNA_1.0.5 ADAPTS_1.0.6 scBio_0.1.6
[4] descend_1.0.0 EpiDISH_2.2.2 TED_1.1
[7] SCDC_0.0.0.9000 MuSiC_0.1.1 deconvSeq_0.3.0
[10] DeconRNASeq_1.28.0 ggplot2_3.3.3 pcaMethods_1.78.0
[13] limSolve_1.5.6 dtangle_2.0.9 MASS_7.3-53.1
[16] FARDEEP_1.0.1 EPIC_1.1.5 nnls_1.4
[19] CellMix_1.6.2 GSEABase_1.48.0 graph_1.64.0
[22] annotate_1.64.0 XML_3.99-0.3 AnnotationDbi_1.48.0
[25] IRanges_2.20.2 S4Vectors_0.24.4 stringr_1.4.0
[28] csSAM_1.2.4 NMF_0.23.0 Biobase_2.46.0
[31] BiocGenerics_0.32.0 cluster_2.1.1 rngtools_1.5
[34] pkgmaker_0.32.2 registry_0.5-1 glmnet_4.1-1
[37] Matrix_1.3-2 Seurat_3.1.2
loaded via a namespace (and not attached):
[1] rsvd_1.0.3 Hmisc_4.5-0
[3] ica_1.0-2 corpcor_1.6.9
[5] class_7.3-18 Rsamtools_2.2.3
[7] foreach_1.5.1 lmtest_0.9-38
[9] crayon_1.4.1 rbibutils_2.0
[11] nlme_3.1-152 backports_1.2.1
[13] rlang_0.4.10 XVector_0.26.0
[15] ROCR_1.0-11 irlba_2.3.3
[17] SparseM_1.81 nloptr_1.2.2.2
[19] limma_3.42.2 scater_1.14.6
[21] L1pack_0.38.196 BiocParallel_1.20.1
[23] bit64_4.0.5 glue_1.4.2
[25] pheatmap_1.0.12 sctransform_0.3.2
[27] vipor_0.4.5 mcmc_0.9-7
[29] tidyselect_1.1.0 SummarizedExperiment_1.16.1
[31] fitdistrplus_1.1-3 tidyr_1.1.3
[33] zoo_1.8-9 GenomicAlignments_1.22.1
[35] xtable_1.8-4 MatrixModels_0.5-0
[37] magrittr_2.0.1 evaluate_0.14
[39] bibtex_0.4.2.3 Rdpack_2.1.1
[41] zlibbioc_1.32.0 sn_1.6-2
[43] rstudioapi_0.13 fastmatrix_0.3-81
[45] rpart_4.1-15 mathjaxr_1.4-0
[47] locfdr_1.1-8 BiocSingular_1.2.2
[49] xfun_0.22 askpass_1.1
[51] multtest_2.42.0 caTools_1.18.1
[53] pbdZMQ_0.3-5 methylKit_1.12.0
[55] tibble_3.1.0 lpSolve_5.6.15
[57] quantreg_5.85 ggrepel_0.9.1
[59] ape_5.4-1 listenv_0.8.0
[61] Biostrings_2.54.0 png_0.1-7
[63] future_1.21.0 withr_2.4.1
[65] bitops_1.0-6 plyr_1.8.6
[67] e1071_1.7-4 dqrng_0.2.1
[69] coda_0.19-4 pillar_1.5.1
[71] gplots_3.1.1 cachem_1.0.4
[73] multcomp_1.4-16 DelayedMatrixStats_1.8.0
[75] vctrs_0.3.6 ellipsis_0.3.1
[77] generics_0.1.0 metap_1.4
[79] tools_3.6.1 foreign_0.8-71
[81] beeswarm_0.3.1 munsell_0.5.0
[83] DelayedArray_0.12.3 fastmap_1.1.0
[85] rtracklayer_1.46.0 plotly_4.9.3
[87] GenomeInfoDbData_1.2.2 gridExtra_2.3
[89] MCMCpack_1.5-0 edgeR_3.28.1
[91] lattice_0.20-41 mutoss_0.1-12
[93] utf8_1.2.1 dplyr_1.0.5
[95] BiocFileCache_1.10.2 jsonlite_1.7.2
[97] scales_1.1.1 pbapply_1.4-3
[99] genefilter_1.68.0 lazyeval_0.2.2
[101] doParallel_1.0.16 latticeExtra_0.6-29
[103] R.utils_2.10.1 reticulate_1.18
[105] checkmate_2.0.0 sandwich_3.0-0
[107] cowplot_1.1.1 statmod_1.4.35
[109] Rtsne_0.15 uwot_0.1.10
[111] igraph_1.2.6 survival_3.2-7
[113] numDeriv_2016.8-1.1 plotrix_3.8-1
[115] htmltools_0.5.1.1 memoise_2.0.0
[117] locfit_1.5-9.4 quadprog_1.5-8
[119] viridisLite_0.3.0 digest_0.6.27
[121] assertthat_0.2.1 rappdirs_0.3.3
[123] repr_1.1.3 emdbook_1.3.12
[125] RSQLite_2.2.4 future.apply_1.7.0
[127] Rmisc_1.5 data.table_1.14.0
[129] blob_1.2.1 R.oo_1.24.0
[131] preprocessCore_1.48.0 splines_3.6.1
[133] Formula_1.2-4 RCurl_1.98-1.2
[135] hms_1.0.0 colorspace_2.0-0
[137] base64enc_0.1-3 BiocManager_1.30.10
[139] mnormt_2.0.2 ggbeeswarm_0.6.0
[141] SDMTools_1.1-221 GenomicRanges_1.38.0
[143] shape_1.4.5 tmvnsim_1.0-2
[145] nnet_7.3-15 Rcpp_1.0.6
[147] mclust_5.4.7 RANN_2.6.1
[149] mvtnorm_1.1-1 fansi_0.4.2
[151] conquer_1.0.2 truncnorm_1.0-8
[153] parallelly_1.23.0 IRdisplay_1.0
[155] R6_2.5.0 ggridges_0.5.3
[157] lifecycle_1.0.0 TFisher_0.2.0
[159] curl_4.3 minqa_1.2.4
[161] xbioc_0.1.19 leiden_0.3.7
[163] qvalue_2.18.0 RcppAnnoy_0.0.18
[165] TH.data_1.0-10 RColorBrewer_1.1-2
[167] iterators_1.0.13 fastseg_1.32.0
[169] htmlwidgets_1.5.3 biomaRt_2.42.1
[171] purrr_0.3.4 globals_0.14.0
[173] openssl_1.4.3 htmlTable_2.1.0
[175] bdsmatrix_1.3-4 codetools_0.2-18
[177] matrixStats_0.58.0 gtools_3.8.2
[179] prettyunits_1.1.1 psych_2.0.12
[181] SingleCellExperiment_1.8.0 dbplyr_2.1.0
[183] gridBase_0.4-7 R.methodsS3_1.8.1
[185] GenomeInfoDb_1.22.1 gtable_0.3.0
[187] tsne_0.1-3 DBI_1.1.1
[189] httr_1.4.2 KernSmooth_2.23-18
[191] stringi_1.5.3 progress_1.2.2
[193] reshape2_1.4.4 uuid_0.1-4
[195] viridis_0.5.1 bbmle_1.0.23.1
[197] boot_1.3-27 IRkernel_1.1.1
[199] BiocNeighbors_1.9.4 lme4_1.1-26
[201] geneplotter_1.64.0 DESeq2_1.26.0
[203] scran_1.14.6 bit_4.0.4
[205] jpeg_0.1-8.1 pkgconfig_2.0.3
[207] Rsolnp_1.16 knitr_1.31
ln -s /nfs/leia/research/ma/chichau/bin/anaconda3/lib/libcrypto.so \
/nfs/leia/research/ma/chichau/bin/anaconda3/x86_64-conda_cos6-linux-gnu/lib
ln -s /nfs/leia/research/ma/chichau/bin/anaconda3/lib/libcurl.so \
/nfs/leia/research/ma/chichau/bin/anaconda3/x86_64-conda_cos6-linux-gnu/lib
ln -s /nfs/leia/research/ma/chichau/bin/anaconda3/lib/libz.so \
/nfs/leia/research/ma/chichau/bin/anaconda3/x86_64-conda_cos6-linux-gnu/lib
ln -s /nfs/leia/research/ma/chichau/bin/anaconda3/lib/libssl.so \
/nfs/leia/research/ma/chichau/bin/anaconda3/x86_64-conda_cos6-linux-gnu/lib
ln -s /nfs/leia/research/ma/chichau/bin/anaconda3/lib/libgfortran.so \
/nfs/leia/research/ma/chichau/bin/anaconda3/x86_64-conda_cos6-linux-gnu/lib
ln -s /nfs/leia/research/ma/chichau/bin/anaconda3/lib/libgomp.so \
/nfs/leia/research/ma/chichau/bin/anaconda3/x86_64-conda_cos6-linux-gnu/lib/
ln -s /nfs/leia/research/ma/chichau/bin/anaconda3/lib/libquadmath.so \
/nfs/leia/research/ma/chichau/bin/anaconda3/x86_64-conda_cos6-linux-gnu/lib/
cd /nfs/leia/research/ma/chichau/bin/anaconda3/lib/R/etc
cp ../../../pkgs/r-base-3.6.1-h9bb98a2_1/lib/R/etc/Makeconf .