nuno-agostinho/ctrap

Identification of candidate causal perturbations from differential gene expression data

cTRAP

cTRAP is an R package designed to compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map (Subramanian et al., Cell 2017). Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

Installing

Bioconductor

cTRAP is available in Bioconductor and can be installed with:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("cTRAP")

GitHub

cTRAP can also be installed from GitHub instead:

install.packages("remotes")
remotes::install_github("nuno-agostinho/cTRAP")

Docker

The Docker images are based on Bioconductor Docker and contain cTRAP and its dependencies.

1. Pull the latest Docker image:

docker pull ghcr.io/nuno-agostinho/ctrap:latest

2. Start RStudio Web from the Docker image:

docker run -e PASSWORD=bioc -p 8787:8787 ghcr.io/nuno-agostinho/ctrap:latest

3. Go to RStudio Web via your web browser at https://localhost:8787
4. Login in RStudio Web with user rstudio and password bioc
5. Load the package in RStudio Web using library(cTRAP)

ctrap's Issues

Replace internal cmapR functions with those from the cmapR R package

https://www.bioconductor.org/packages/release/bioc/html/cmapR.html

Problems with compareAgainstL1000

Hi,

for some reason, when I am running the same code from this pdf, when I execute the line:

compareSmallMolecule$spearman <- compareAgainstL1000( diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="spearman")

I am getting the following error:

Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed

What might be the problem?

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] dplyr_0.7.8 cTRAP_1.0.2 biomaRt_2.38.0 Biobase_2.42.0 BiocGenerics_0.28.0 DeMAND_1.12.0
[7] KernSmooth_2.23-15 limma_3.38.2

loaded via a namespace (and not attached):
[1] httr_1.3.1 jsonlite_1.5 bit64_0.9-7 R.utils_2.7.0 gtools_3.8.1
[6] assertthat_0.2.0 stats4_3.5.1 blob_1.1.1 yaml_2.2.0 progress_1.2.0
[11] slam_0.1-43 pillar_1.3.0 RSQLite_2.1.1 lattice_0.20-35 glue_1.3.0
[16] digest_0.6.18 colorspace_1.3-2 cowplot_0.9.3 Matrix_1.2-14 R.oo_1.22.0
[21] plyr_1.8.4 XML_3.98-1.16 pkgconfig_2.0.2 purrr_0.2.5 relations_0.6-8
[26] scales_1.0.0 gdata_2.18.0 BiocParallel_1.16.0 tibble_1.4.2 IRanges_2.16.0
[31] ggplot2_3.1.0 pbapply_1.3-4 lazyeval_0.2.1 magrittr_1.5 crayon_1.3.4
[36] memoise_1.1.0 R.methodsS3_1.7.1 gplots_3.0.1 tools_3.5.1 data.table_1.11.8
[41] prettyunits_1.0.2 hms_0.4.2 stringr_1.3.1 Rhdf5lib_1.4.0 S4Vectors_0.20.1
[46] munsell_0.5.0 cluster_2.0.7-1 AnnotationDbi_1.44.0 bindrcpp_0.2.2 compiler_3.5.1
[51] caTools_1.17.1.1 rlang_0.3.0.1 rhdf5_2.26.0 grid_3.5.1 RCurl_1.95-4.11
[56] marray_1.60.0 igraph_1.2.2 bitops_1.0-6 gtable_0.2.0 curl_3.2
[61] DBI_1.0.0 sets_1.0-18 R6_2.3.0 gridExtra_2.3 knitr_1.20
[66] bit_1.1-14 bindr_0.1.1 fastmatch_1.1-0 fgsea_1.8.0 readr_1.1.1
[71] stringi_1.2.4 Rcpp_1.0.0 piano_1.22.0 tidyselect_0.2.5

Update Dockerfile to use newer Bioconductor Docker image

See https://hub.docker.com/r/bioconductor/bioconductor_docker to update the following line to use the appropriate Docker image:

cTRAP/Dockerfile

Line 1 in d6be0a1

FROM bioconductor/release_base2:latest

Using Seurat or scRNA-seq data

Do you have a vignette tutorial code on how to use cTRAP on Seurat or scRNA-seq data please? Thank you!

error in loadCMapZscores

Hi I was going through the tutorial and ran into this error:

zscores <- loadCMapZscores(perts[ , 1:10])
Loading data from /home/shared/Misc_studies/CMap_DepMap/cmapZscores.gctx...
Error in .local(.Object, ...) : unused argument (verbose = verbose)

Pls advise. Thank you.

cTRAP not working properly with demo data

Issue Summary

Hi Nuno,

I've encountered some issues with the cTRAP WebApp and the R package. Here are the details:

WebApp Issue:

The WebApp version of cTRAP, hosted here, is not working properly. After uploading Differentially Expression Data and loading cMAP Perturbations, attempting to perform an analysis by clicking on "Rank by similarity" results in the site getting a grey filter and loading indefinitely:

R Package Issue:

After following the R tutorial for the cTRAP R package, the plotTargetingDrugsVSsimilarPerturbations function is not working as intended:

plotTargetingDrugsVSsimilarPerturbations(predicted, compareCompounds, column="spearman_rank")

#Resulting on the following error
> Columns 'broad id' and 'pubchem_cid' were matched based on 0 common values; to manually select columns to compare, please set arguments starting with 'keyCol'

I encounter both these errors when using the default Differentially Expression Data (diffExprStat) from the R package.

Thank you for your attention and your help!

Best regards,
Alex