Introduction | Samples and Sequencing | Read Mapping and Read Assignment | Junction Detection | TaqMan RT-PCR | Citation | Authors | Contact
Package: seqc 1.47.0
Yang Liao
seqc: RNA-seq data generated from SEQC (MAQC-III) study
The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well.
Authors:
seqc_1.47.0.tar.gz
seqc_1.47.0.tar.gz(r-4.7-any)seqc_1.47.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
seqc/json (API)
| # Install 'seqc' in R: |
| install.packages('seqc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- ILM_aceview_gene_AGR - Read count tables from the SEQC project
- ILM_aceview_gene_BGI - Read count tables from the SEQC project
- ILM_aceview_gene_CNL - Read count tables from the SEQC project
- ILM_aceview_gene_COH - Read count tables from the SEQC project
- ILM_aceview_gene_MAY - Read count tables from the SEQC project
- ILM_aceview_gene_NVS - Read count tables from the SEQC project
- ILM_junction_AGR_A - Junction tables from the SEQC project
- ILM_junction_AGR_B - Junction tables from the SEQC project
- ILM_junction_AGR_C - Junction tables from the SEQC project
- ILM_junction_AGR_D - Junction tables from the SEQC project
- ILM_junction_BGI_A - Junction tables from the SEQC project
- ILM_junction_BGI_B - Junction tables from the SEQC project
- ILM_junction_BGI_C - Junction tables from the SEQC project
- ILM_junction_BGI_D - Junction tables from the SEQC project
- ILM_junction_CNL_A - Junction tables from the SEQC project
- ILM_junction_CNL_B - Junction tables from the SEQC project
- ILM_junction_CNL_C - Junction tables from the SEQC project
- ILM_junction_CNL_D - Junction tables from the SEQC project
- ILM_junction_COH_A - Junction tables from the SEQC project
- ILM_junction_COH_B - Junction tables from the SEQC project
- ILM_junction_COH_C - Junction tables from the SEQC project
- ILM_junction_COH_D - Junction tables from the SEQC project
- ILM_junction_MAY_A - Junction tables from the SEQC project
- ILM_junction_MAY_B - Junction tables from the SEQC project
- ILM_junction_MAY_C - Junction tables from the SEQC project
- ILM_junction_MAY_D - Junction tables from the SEQC project
- ILM_junction_NVS_A - Junction tables from the SEQC project
- ILM_junction_NVS_B - Junction tables from the SEQC project
- ILM_junction_NVS_C - Junction tables from the SEQC project
- ILM_junction_NVS_D - Junction tables from the SEQC project
- ILM_refseq_gene_AGR - Read count tables from the SEQC project
- ILM_refseq_gene_BGI - Read count tables from the SEQC project
- ILM_refseq_gene_CNL - Read count tables from the SEQC project
- ILM_refseq_gene_COH - Read count tables from the SEQC project
- ILM_refseq_gene_MAY - Read count tables from the SEQC project
- ILM_refseq_gene_NVS - Read count tables from the SEQC project
- LIF_aceview_gene_LIV - Read count tables from the SEQC project
- LIF_aceview_gene_NWU - Read count tables from the SEQC project
- LIF_aceview_gene_PSU - Read count tables from the SEQC project
- LIF_aceview_gene_SQW - Read count tables from the SEQC project
- LIF_junction_LIV_A - Junction tables from the SEQC project
- LIF_junction_LIV_B - Junction tables from the SEQC project
- LIF_junction_LIV_C - Junction tables from the SEQC project
- LIF_junction_LIV_D - Junction tables from the SEQC project
- LIF_junction_NWU_A - Junction tables from the SEQC project
- LIF_junction_NWU_B - Junction tables from the SEQC project
- LIF_junction_NWU_C - Junction tables from the SEQC project
- LIF_junction_NWU_D - Junction tables from the SEQC project
- LIF_junction_PSU_A - Junction tables from the SEQC project
- LIF_junction_PSU_B - Junction tables from the SEQC project
- LIF_junction_PSU_C - Junction tables from the SEQC project
- LIF_junction_PSU_D - Junction tables from the SEQC project
- LIF_junction_SQW_A - Junction tables from the SEQC project
- LIF_junction_SQW_B - Junction tables from the SEQC project
- LIF_junction_SQW_C - Junction tables from the SEQC project
- LIF_junction_SQW_D - Junction tables from the SEQC project
- LIF_refseq_gene_LIV - Read count tables from the SEQC project
- LIF_refseq_gene_NWU - Read count tables from the SEQC project
- LIF_refseq_gene_PSU - Read count tables from the SEQC project
- LIF_refseq_gene_SQW - Read count tables from the SEQC project
- ROC_aceview_gene_MGP - Read count tables from the SEQC project
- ROC_aceview_gene_NYU - Read count tables from the SEQC project
- ROC_aceview_gene_SQW - Read count tables from the SEQC project
- ROC_junction_MGP_A - Junction tables from the SEQC project
- ROC_junction_MGP_B - Junction tables from the SEQC project
- ROC_junction_NYU_A - Junction tables from the SEQC project
- ROC_junction_NYU_B - Junction tables from the SEQC project
- ROC_junction_SQW_A - Junction tables from the SEQC project
- ROC_junction_SQW_B - Junction tables from the SEQC project
- ROC_refseq_gene_MGP - Read count tables from the SEQC project
- ROC_refseq_gene_NYU - Read count tables from the SEQC project
- ROC_refseq_gene_SQW - Read count tables from the SEQC project
- taqman - TaqMan RT-PCR results from the SEQC project
On BioConductor:seqc-1.47.0(data/experiment 3.24)seqc-1.46.0(data/experiment 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
experimentdatarnaseqdataqpcrdatasequencingdatadatapkg
Last updated from:5c7a89af20. Checks:1 ERROR, 2 WARNING, 1 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 206 | ||
| linux-devel | WARNING | 334 | ||
| source / vignettes | OK | 1322 | ||
| linux-release | WARNING | 299 |
Exports:seqc.eSetseqc.samples
Dependencies:BiobaseBiocGenericsgenerics
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| RNA-seq data employed in the Sequence Quality Control (SEQC) Project | SEQC-package seqc-package SEQC seqc |
| Read count tables from the SEQC project | ILM_aceview_gene_AGR ILM_aceview_gene_BGI ILM_aceview_gene_CNL ILM_aceview_gene_COH ILM_aceview_gene_MAY ILM_aceview_gene_NVS ILM_refseq_gene_AGR ILM_refseq_gene_BGI ILM_refseq_gene_CNL ILM_refseq_gene_COH ILM_refseq_gene_MAY ILM_refseq_gene_NVS LIF_aceview_gene_LIV LIF_aceview_gene_NWU LIF_aceview_gene_PSU LIF_aceview_gene_SQW LIF_refseq_gene_LIV LIF_refseq_gene_NWU LIF_refseq_gene_PSU LIF_refseq_gene_SQW ROC_aceview_gene_MGP ROC_aceview_gene_NYU ROC_aceview_gene_SQW ROC_refseq_gene_MGP ROC_refseq_gene_NYU ROC_refseq_gene_SQW |
| Junction tables from the SEQC project | ILM_junction_AGR_A ILM_junction_AGR_B ILM_junction_AGR_C ILM_junction_AGR_D ILM_junction_BGI_A ILM_junction_BGI_B ILM_junction_BGI_C ILM_junction_BGI_D ILM_junction_CNL_A ILM_junction_CNL_B ILM_junction_CNL_C ILM_junction_CNL_D ILM_junction_COH_A ILM_junction_COH_B ILM_junction_COH_C ILM_junction_COH_D ILM_junction_MAY_A ILM_junction_MAY_B ILM_junction_MAY_C ILM_junction_MAY_D ILM_junction_NVS_A ILM_junction_NVS_B ILM_junction_NVS_C ILM_junction_NVS_D LIF_junction_LIV_A LIF_junction_LIV_B LIF_junction_LIV_C LIF_junction_LIV_D LIF_junction_NWU_A LIF_junction_NWU_B LIF_junction_NWU_C LIF_junction_NWU_D LIF_junction_PSU_A LIF_junction_PSU_B LIF_junction_PSU_C LIF_junction_PSU_D LIF_junction_SQW_A LIF_junction_SQW_B LIF_junction_SQW_C LIF_junction_SQW_D ROC_junction_MGP_A ROC_junction_MGP_B ROC_junction_NYU_A ROC_junction_NYU_B ROC_junction_SQW_A ROC_junction_SQW_B |
| Create an ExpressionSet of counts for a given subset of the samples provided by the seqc data package | seqc.eSet |
| Return a character vector of the available SEQC samples | seqc.samples |
| TaqMan RT-PCR results from the SEQC project | taqman |