Hi,
I successfully installed NoRCE on 2 different systems, and tried running the example code. Each time I get the same error.
"Error in assembly(org_assembly) :
Install package TxDb.Hsapiens.UCSC.hg19.knownGene in order to use this function."
I have installed the TxDb.Hsapiens.UCSC.hg19.knownGene package and imported the library also, before running the example code. Still getting same error. Can you please help, what mistake I am doing?

Here is my session Info.
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS/LAPACK: /home/R-4/lib/libopenblasp-r0.3.12.so

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

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

other attached packages:
[1] NoRCE_1.2.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5
[2] lattice_0.20-41
[3] GO.db_3.12.1
[4] prettyunits_1.1.1
[5] Rsamtools_2.6.0
[6] Biostrings_2.58.0
[7] assertthat_0.2.1
[8] digest_0.6.27
[9] BiocFileCache_1.14.0
[10] plyr_1.8.6
[11] R6_2.5.0
[12] GenomeInfoDb_1.26.0
[13] stats4_4.0.3
[14] RSQLite_2.2.1
[15] ggplot2_3.3.2
[16] httr_1.4.2
[17] pillar_1.4.6
[18] zlibbioc_1.36.0
[19] rlang_0.4.8
[20] GenomicFeatures_1.42.1
[21] progress_1.2.2
[22] curl_4.3
[23] blob_1.2.1
[24] S4Vectors_0.28.0
[25] Matrix_1.2-18
[26] BiocParallel_1.24.1
[27] readr_1.4.0
[28] stringr_1.4.0
[29] igraph_1.2.6
[30] munsell_0.5.0
[31] RCurl_1.98-1.2
[32] bit_4.0.4
[33] biomaRt_2.46.0
[34] DelayedArray_0.16.0
[35] compiler_4.0.3
[36] rtracklayer_1.50.0
[37] pkgconfig_2.0.3
[38] askpass_1.1
[39] BiocGenerics_0.36.0
[40] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[41] openssl_1.4.3
[42] tidyselect_1.1.0
[43] SummarizedExperiment_1.20.0
[44] tibble_3.0.4
[45] GenomeInfoDbData_1.2.4
[46] IRanges_2.24.0
[47] matrixStats_0.57.0
[48] XML_3.99-0.5
[49] crayon_1.3.4
[50] dplyr_1.0.2
[51] dbplyr_2.0.0
[52] GenomicAlignments_1.26.0
[53] bitops_1.0-6
[54] rappdirs_0.3.1
[55] grid_4.0.3
[56] gtable_0.3.0
[57] lifecycle_0.2.0
[58] DBI_1.1.0
[59] magrittr_1.5
[60] scales_1.1.1
[61] stringi_1.5.3
[62] reshape2_1.4.4
[63] XVector_0.30.0
[64] xml2_1.3.2
[65] ellipsis_0.3.1
[66] generics_0.1.0
[67] vctrs_0.3.4
[68] tools_4.0.3
[69] bit64_4.0.5
[70] Biobase_2.50.0
[71] glue_1.4.2
[72] purrr_0.3.4
[73] hms_0.5.3
[74] MatrixGenerics_1.2.0
[75] parallel_4.0.3
[76] colorspace_2.0-0
[77] AnnotationDbi_1.52.0
[78] GenomicRanges_1.42.0
[79] memoise_1.1.0

Hi

I have a dataset as follows: 2 Ctrl samples, 2 KO samples of isoform 1 of GeneA, and 2 KO samples of Isoform2 of GeneA.

KO of isoform1 results in a lot of lncRNA and other ncRNAs being differentially regulated as compared to KO of Isoform2.

Is it fine to use your tool on TotalRNAseq data? I wish to see which ncRNAs might be interesting to study further and use geneGOEnricher but I am confused as to whether I should only use the KO sample matrix when specifying the following inputs exp1 = mirna, exp2 = mrna? Also, should I supply raw counts or normalized counts?

I am using the BioConductor package and I keep getting the following error:

Error in stop_if_wrong_length(what, ans_len) :
'ranges' must have the length of the object to construct (1) or length 1

when I run the command:

geneGOEnricher(gene = my_ensembl_genes, genetype = "Ensembl_gene", org_assembly = "mm10", near = TRUE)

There is also a warning message:
'track' parameter is deprecated now you go by the 'table' instead
use ucscTables(genome, track) to retrieve the list of tables for a track

I managed to get results once but now I consistently get the error.

Hello, I have already succesfully used the geneGOEnricher function of the NoRCE package in the past but now it seems there is an issue even when I use sample code as reported in the package helps.
Please you can see also the post at Bioconductor Support site https://support.bioconductor.org/p/9159738/

It it possible to fix this error?

Thanks in advance!