conda install r-rnasum==0.0.X -c umccr -c conda-forge -c bioconda
conda install r-rnasum==X.X.X -c umccr -c conda-forge -c bioconda
The table below lists all input data accepted in RNAsum:
RNAsum
rnasum_cli=$(Rscript -e 'x = system.file("cli", package = "RNAsum"); cat(x, "\n")' | xargs) export PATH="${rnasum_cli}:${PATH}"
$ rnasum.R --version -1.1.0 +1.1.5 $ rnasum.R --help Usage ===== -/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RNAsum/cli/rnasum.R [options] +/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RNAsum/cli/rnasum.R [options] Options @@ -337,47 +337,47 @@ Usage --log Log2 transform data before normalisation. ---manta_tsv=MANTA_TSV - File path to umccrise 'manta.tsv' output. +--norm=NORM + Normalisation method. ---norm=NORM - Normalisation method. +--pcgr_splice_vars + Include non-coding splice region variants reported in PCGR. ---pcgr_splice_vars - Include non-coding splice region variants reported in PCGR. +--pcgr_tier=PCGR_TIER + Tier threshold for reporting variants reported in PCGR. [def: 4] ---pcgr_tier=PCGR_TIER - Tier threshold for reporting variants reported in PCGR. [def: 4] +--pcgr_tiers_tsv=PCGR_TIERS_TSV + File path to PCGR 'snvs_indels.tiers.tsv' output. ---pcgr_tiers_tsv=PCGR_TIERS_TSV - File path to PCGR 'snvs_indels.tiers.tsv' output. +--project=PROJECT + Project name, used for annotation purposes only. ---project=PROJECT - Project name, used for annotation purposes only. +--purple_gene_tsv=PURPLE_GENE_TSV + File path to PURPLE 'purple.cnv.gene.tsv' output. ---purple_gene_tsv=PURPLE_GENE_TSV - File path to PURPLE 'purple.cnv.gene.tsv' output. +--report_dir=REPORT_DIR + Directory path to output report. ---report_dir=REPORT_DIR - Directory path to output report. +--salmon=SALMON + File path to salmon 'quant.genes.sf' output. ---salmon=SALMON - File path to salmon 'quant.genes.sf' output. +--sample_name=SAMPLE_NAME + Sample name to be presented in report. ---sample_name=SAMPLE_NAME - Sample name to be presented in report. +--sample_source=SAMPLE_SOURCE + Type of investigated sample. [def: -] ---sample_source=SAMPLE_SOURCE - Type of investigated sample. [def: -] +--save_tables + Save interactive summary tables as HTML. ---save_tables - Save interactive summary tables as HTML. +--scaling=SCALING + Scaling for z-score transformation (gene-wise or group-wise). [def: gene-wise] ---scaling=SCALING - Scaling for z-score transformation (gene-wise or group-wise). [def: gene-wise] +--subject_id=SUBJECT_ID + Subject ID. ---subject_id=SUBJECT_ID - Subject ID. +--sv_tsv=SV_TSV + File path to text file with genes related to structural variation. --top_genes=TOP_GENES Number of top ranked genes to be presented in report. diff --git a/pkgdown.yml b/pkgdown.yml index c9e274c9..de818b0a 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -7,7 +7,7 @@ articles: report_structure: report_structure.html tcga_projects_summary: tcga_projects_summary.html workflow: workflow.html -last_built: 2024-11-08T00:45Z +last_built: 2024-11-08T01:54Z urls: reference: https://umccr.github.io/rnasum/reference article: https://umccr.github.io/rnasum/articles diff --git a/reference/CapStr.html b/reference/CapStr.html index 355912fc..052d2048 100644 --- a/reference/CapStr.html +++ b/reference/CapStr.html @@ -10,7 +10,7 @@ RNAsum - 1.1.4 + 1.1.5 diff --git a/reference/REFERENCE_DATASETS.html b/reference/REFERENCE_DATASETS.html index 7d0be164..07a39f9d 100644 --- a/reference/REFERENCE_DATASETS.html +++ b/reference/REFERENCE_DATASETS.html @@ -10,7 +10,7 @@ RNAsum - 1.1.4 + 1.1.5 diff --git a/reference/RNAsum-package.html b/reference/RNAsum-package.html index 47135034..106de41b 100644 --- a/reference/RNAsum-package.html +++ b/reference/RNAsum-package.html @@ -10,7 +10,7 @@ RNAsum - 1.1.4 + 1.1.5 diff --git a/reference/arriba_pdf_read.html b/reference/arriba_pdf_read.html index 3d045b65..b18df09c 100644 --- a/reference/arriba_pdf_read.html +++ b/reference/arriba_pdf_read.html @@ -12,7 +12,7 @@ RNAsum - 1.1.4 + 1.1.5 @@ -95,10 +95,10 @@ Examples#> # A tibble: 4 × 2 #> nm png #> <chr> <chr> -#> 1 EP300.AS1__XRCC6_chr22.41195482_chr22.41636113 /tmp/RtmpQ… -#> 2 LAPTM4A__AC098828.3_chr2.20051410_chr2.20064511 /tmp/RtmpQ… -#> 3 FNIP1__AC112492.1.83716..DCAF8L1.218._chr5.131642783_chrX.27977775 /tmp/RtmpQ… -#> 4 ZFP64__MORC2_chr20.52096811_chr22.30963497 /tmp/RtmpQ… +#> 1 EP300.AS1__XRCC6_chr22.41195482_chr22.41636113 /tmp/RtmpH… +#> 2 LAPTM4A__AC098828.3_chr2.20051410_chr2.20064511 /tmp/RtmpH… +#> 3 FNIP1__AC112492.1.83716..DCAF8L1.218._chr5.131642783_chrX.27977775 /tmp/RtmpH… +#> 4 ZFP64__MORC2_chr20.52096811_chr22.30963497 /tmp/RtmpH…