1 Mapping statistics | 2 Identifying variable genes | 3 Number of TRA genes detected per cell compared to the number of genes. | 4 Variable genes are enriched for TRA genes | 5 Both Aire-dependent and Aire-independent TRAs are expressed at low frequencies in single mTECs | 6 Gene-gene correlation analyses | 7 Data analysis for TRA-selected cells | 8 Co-expressed genes tend to be clustered in the genome | 9 ATAC-seq data | 10 Session Information
Package: Single.mTEC.Transcriptomes 1.41.1
Alejandro Reyes
Single.mTEC.Transcriptomes: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells
This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript.
Authors:
Single.mTEC.Transcriptomes_1.41.1.tar.gz
Single.mTEC.Transcriptomes_1.41.1.tar.gz(r-4.7-any)Single.mTEC.Transcriptomes_1.41.1.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Single.mTEC.Transcriptomes/json (API)
| # Install 'Single.mTEC.Transcriptomes' in R: |
| install.packages('Single.mTEC.Transcriptomes', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- aireDependentSansom - List of Aire-dependent genes
- biotype - Mouse biotypes
- biotype - Mouse biotypes
- cea1Coexpression - Cea1 co-expression group data
- corMatSp - Gene-gene correlation network
- corMatSpNoMarker - Gene-gene correlation network
- deGenesNone - Highly variable genes.
- deGenesSansom - Highly variable genes from Sansom et al.
- dxd - Count data from the single-mTEC data.
- dxdATAC - ATAC-seq summarized counts.
- dxdFANTOM - FANTOM dataset
- geneNames - Mouse gene names
- geneNames - Mouse gene names
- geneRanges - Genomic range coordinates.
- muc1Coexpression - Muc1 co-expression group data
- nomarkerCellsClustering - Clustering results
- percentsGG - Mapping statistics
- permsAllClusters - Permutation results
- realAllClusters - Permutation results
- tras - Tissue restricted antigens lists.
- Ycorr - Output from scLVM
On BioConductor:Single.mTEC.Transcriptomes-1.41.1(data/experiment 3.24)Single.mTEC.Transcriptomes-1.40.0(data/experiment 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:ca9a870091. Checks:1 ERROR, 1 WARNING, 1 OK, 1 NOTE. 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 | 243 | ||
| linux-devel | WARNING | 543 | ||
| source / vignettes | OK | 3926 | ||
| linux-release | NOTE | 663 |
Exports:
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Single-cell transcriptome data of medullary thymic epithelial cells | Single.mTec.Transcriptomes-package |
| List of Aire-dependent genes | aireDependentSansom |
| Mouse biotypes | biotype |
| Human biotypes | biotypesHuman |
| Cea1 co-expression group data | cea1Coexpression |
| Gene-gene correlation network | corMatsNoMarker corMatSp corMatSpNoMarker |
| Highly variable genes. | deGenesNone |
| Highly variable genes from Sansom et al. | deGenesSansom |
| ATAC-seq summarized counts. | dxdATAC |
| FANTOM dataset | dxdFANTOM fantom |
| Mouse gene names | geneNames |
| Human gene names | geneNamesHuman |
| Genomic range coordinates. | geneRanges |
| Count data from the single-mTEC data. | dxd mTECdxd |
| Muc1 co-expression group data | muc1Coexpression |
| Clustering results | nomarkerCellsClustering |
| Mapping statistics | percentsGG |
| Permutation results | permsAllClusters permutationResults realAllClusters |
| Output from scLVM | beta beta0 h5GeneNames heter scLVM_output vars Ycorr |
| Tissue restricted antigens lists. | tras |