geneSets.RdReference gene sets consolidated from numerous sources to faciliate cell annotation and module scoring.
data(geneSets)A list of data.frames containing the following genesets:
Cancer single-cell state atlas
Cell marker atlas: Manually-curated celltype-specific gene sets from over 100,000 published papers. (Zhang et al. (2019) Nucleic Acids Res.)
Core cytotoxic T lymphocyte kill genes. (Lawson et al. (2020)
Cell-cycle markers (Tirosh et al. (2016) Science)
Glioblastoma-subtype specific markers (Neftel et al. (2019) Cell)
Immune cell signatures for 7 immune cell types identified in tumors using scRNAseq (Nirmal et el. (2018) Cancer Immunol Res.)
Top 50 differentially-markers for each cell in Mouse organogenesis cell atlas characterized using scRNAseq. (Cao et al. (2019) Nature)
Top 100 differentially-markers for each cell in Mouse organogenesis cell atlas characterized using scRNAseq. (Cao et al. (2019) Nature)
Neural differential markers provided by Hong Han.
Murine cell-type specific markers consolidated from multiple studies through unified framework. (Franzen et al. (2019) Database (Oxford))
Human cell-type specific markers consolidated from multiple studies through unified framework. (Franzen et al. (2019) Database (Oxford))
Murine kidney cell-specific markers (Park et al. (2018) Science)
Murine-specific trancription factor genesets; TRRUSTv2 database. (Han et al. (2018) Nucleic Acid Res.)
Human-specific trancription factor genesets; TRRUSTv2 database. (Han et al. (2018) Nucleic Acid Res.)
Murine-specific trancription factor genesets, with regulatory annotation (i.e., activating vs repressing); TRRUSTv2 database. (Han et al. (2018) Nucleic Acid Res.)
Human-specific trancription factor genesets, with regulatory annotation (i.e., activating vs repressing); TRRUSTv2 database. (Han et al. (2018) Nucleic Acid Res.)
Bulk RNAseq-derived cell-specific markers (Tapial et al. (2017) Genome Res.)
Tumor immunesubtype markers (Thorsson et al. (2018) Immunity)
Immune marker panels obtained from literature review
universal marker panels obtained from literature review
cancer marker panels obtained from literature review
Animal transcription factor database. List of human and murine transcription factors
Glioblastoma stem cell injury response and developmental genesets. Single cell derived.
Glioblastoma stem cell injury response and developmental genesets. Bulk RNA derived.
Neural cell gene panels
Astrocyte gene panels, specifically A1 and A2 reactive astrocyte markers
Neural cell gene panels
Verhaak GBM-subtype genesets
Immune-related gene markers reported in Table S4 of Combes 2022
Immune-related gene markers reported in Table S5 of Combes 2022
Cell-type markers derived from public scRNAseq atlases.
Cell-type specific marker genes used by CancerSCEM.
Stemness markers, literature curated. Sources include (StemChecker, Malta, Hong, Mikkelsen, Palmer, Bhattacharya, Dong, Pece, Feng, Schulten)
50 “hallmark” gene sets from the Molecular Signature Database (MSigDB)
Transcriptional hallmarks of intra-tumor heterogeneity
Glioma stem cell (GSC)-associated gene markers
Mass Spectrometric-Derived Cell Surface Protein Atlas
An anatomic transcriptional atlas of human glioblastoma (IVY GBM)
data(geneSets)
# retrieve geneset
cell_catalog <- geneSets[["Cell_Catalog"]]
# convert wide dataframe format to named list format
call_catalog.list <- wideDF2namedList(cell_catalog)