Support Drosophila melanogaster?

[ashleymaeconard]

Hello! I have enjoyed using ENCODExplorer but I would like to query for Drosophila melanogaster. I tried using the organism, assembly, and biosample_type. Do you support other organisms besides Homo sapiens and Mus musculus?
I have been following:
https://bioconductor.org/packages/release/bioc/vignettes/ENCODExplorer/inst/doc/ENCODExplorer.html and http://bioconductor.org/packages/release/bioc/manuals/ENCODExplorer/man/ENCODExplorer.pdf

[ashleymaeconard]

I should be more clear - I see
> query<-queryEncode(organism="Drosophila melanogaster") Results : 11757 files, 503 datasets

however when for example searching:
grep("cwo", query$target) integer(0)
even though on encodeproject.org I do have results: namely ENCSR900TNL

[ericfournier2]

Hi, if you try:

queryEncodeGeneric(accession="ENCSR900TNL")

you will find that ENCODE lists the target for those experiments as "eGFP-cwo", which means that exact searches for target="cwo" will fail. Using fuzzy search would solve this issue:

queryEncodeGeneric(organism="Drosophila melanogaster", target="cwo", fuzzy=TRUE)

This works on my end.

As an aside, if you're looking for peak information rather than raw ChIP data, you might find the queryConsensusPeaks and buildConsensusPeaks functions useful.

Cheers,

[ashleymaeconard]

Hello again! Thank you for your prompt response! For ENCODExplorer_2.4.0 I do not have queryEncodeGeneric. I am using R 3.6 and tried installing through bioconductor, then conda. Neither worked. I followed this closed post to install ENCODExplorer_2.4.0:#42 (comment)

> library(ENCODExplorer)
> query
query        query_res    queryEncode

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS/LAPACK: /Users/ashleymaeconard/anaconda2/envs/timeor_env2/lib/R/lib/libRblas.dylib

Random number generation:
 RNG:     Mersenne-Twister
 Normal:  Inversion
 Sample:  Rounding

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] purrr_0.3.3         modeest_2.4.0       dplyr_0.8.4
 [4] stringr_1.4.0       RcisTarget_1.6.0    data.table_1.12.8
 [7] visNetwork_2.0.9    doRNG_1.8.2         rngtools_1.5
[10] doMC_1.3.6          iterators_1.0.12    foreach_1.4.8
[13] ENCODExplorer_2.4.0 shinythemes_1.1.2   DT_0.12
[16] shiny_1.3.2

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                matrixStats_0.55.0
 [3] bit64_0.9-7                 GenomeInfoDb_1.22.0
 [5] fBasics_3042.89             tools_3.6.1
 [7] utf8_1.1.4                  R6_2.4.1
 [9] rpart_4.1-15                DBI_1.1.0
[11] BiocGenerics_0.32.0         tidyselect_1.0.0
[13] timeSeries_3062.100         bit_1.1-15.2
[15] compiler_3.6.1              AUCell_1.8.0
[17] cli_2.0.1                   graph_1.64.0
[19] Biobase_2.46.0              DelayedArray_0.12.2
[21] spatial_7.3-11              digest_0.6.24
[23] R.utils_2.9.2               XVector_0.26.0
[25] pkgconfig_2.0.3             htmltools_0.4.0
[27] stabledist_0.7-1            htmlwidgets_1.5.1
[29] rlang_0.4.4                 RSQLite_2.2.0
[31] zoo_1.8-7                   jsonlite_1.6.1
[33] crosstalk_1.0.0             BiocParallel_1.20.1
[35] R.oo_1.23.0                 RCurl_1.95-4.12
[37] magrittr_1.5                feather_0.3.5
[39] GenomeInfoDbData_1.2.2      Matrix_1.2-18
[41] Rcpp_1.0.3                  S4Vectors_0.24.3
[43] fansi_0.4.1                 lifecycle_0.1.0
[45] R.methodsS3_1.8.0           stringi_1.4.3
[47] yaml_2.2.1                  SummarizedExperiment_1.16.1
[49] stable_1.1.4                zlibbioc_1.32.0
[51] grid_3.6.1                  blob_1.2.1
[53] promises_1.1.0              crayon_1.3.4
[55] lattice_0.20-38             annotate_1.64.0
[57] hms_0.5.3                   pillar_1.4.3
[59] GenomicRanges_1.38.0        statip_0.2.3
[61] codetools_0.2-16            rmutil_1.1.3
[63] stats4_3.6.1                XML_3.98-1.19
[65] glue_1.3.1                  vctrs_0.2.2
[67] httpuv_1.5.1                tidyr_1.0.2
[69] clue_0.3-57                 assertthat_0.2.1
[71] mime_0.9                    xtable_1.8-4
[73] later_1.0.0                 timeDate_3043.102
[75] tibble_2.1.3                AnnotationDbi_1.48.0
[77] memoise_1.1.0               IRanges_2.20.2
[79] cluster_2.1.0               GSEABase_1.48.0

In the tutorial I see that fuzzy is used as a parameter to queryEncode() however when looking at the code itself and trying it for ENCODExplorer_2.4.1 it is not a parameter that I can use:

> queryEncode
function (df = NULL, set_accession = NULL, assay = NULL, biosample_name = NULL,
    dataset_accession = NULL, file_accession = NULL, file_format = NULL,
    lab = NULL, organism = NULL, target = NULL, treatment = NULL,
    project = NULL, biosample_type = NULL, file_status = "released",
    status = "released", fixed = TRUE, quiet = FALSE)
...

[ericfournier2]

The latest release of BioConductor needs R >= 3.6, so there is no reason you shouldn't be able to installl it. I think you may have confused BioConductor release 3.6 and R release 3.6.

You can find the instructions for installing ENCODExplorer on the BioConductor page: https://bioconductor.org/packages/release/bioc/html/ENCODExplorer.html

[ashleymaeconard]

Hi, do you have a version of ENCODExplorer that is compatible for R 3.6 which has queryEncodeGeneric? I had loaded ENCODExplorer 2.12.1 and it worked fine to use queryEncodeGeneric but now it seems that it has been removed from bioconductor https://bioconductor.org/help/search/index.html?q=ENCODExplorer/. And thank you for your comment about the BioConductor release 3.6 vs. R release 3.6. I am aware that they are different.