| Title: | data set for R package seq2pathway |
|---|---|
| Description: | Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project. |
| Authors: | Bin Wang <[email protected]> |
| Maintainer: | Arjun Kinstlick <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.44.0 |
| Built: | 2026-10-10 11:07:28 UTC |
| Source: | https://github.com/bioc/seq2pathway.data |
demo result of gene2pathway function from chip seq data
data("dat_gene2path_chip")data("dat_gene2path_chip")
A list with 2 elements.
gene2pathway_result.2a list of gene2pathway test result, with 3 data frames(3 GO terms)
gene2pathway_result.FETa list of fisher's test result, with 3 data frames(3 GO terms)
A list, with two sub lists. The name of one sub list is "gene2pathway_result.2", with 3 data frames of GO_BP, GO_MF, and GO_CC, another is "gene2pathway_result.FET", with 3 dara frames of GO_BP, GO_MF, and GO_CC.
demo result of gene2pathway function from RNA seq data
data("dat_gene2path_RNA")data("dat_gene2path_RNA")
A list with 2 elements.
gene2pathway_result.2a data frame of gene2pathway test result
gene2pathway_result.FETa data frame of fisher's test result
A list, with two elements. one element is a data frame about "gene2pathway_result.2"", another data frame is about "gene2pathway_result.FET".
demo result of seq2pathway function from chip seq data
data("dat_seq2pathway_GOterms")data("dat_seq2pathway_GOterms")
A list with 3 elements.
seq2gene_resulta list with 2 annotation table
gene2pathway_result.FAIMEa list of gene2pathway test result, with 3 data frames(3 GO terms)
gene2pathway_result.FETa list of fisher's test result, with 3 data frames(3 GO terms)
A list, with three sub lists. The name of first sub list is seq2gene_result, with 2 data frames of full and coding gene annotation respectively, the name of second sub list is "gene2pathway_result.FAIME", with 3 data frames of GO_BP, GO_MF, and GO_CC, the third is "gene2pathway_result.FET", with 3 dara frames of GO_BP, GO_MF, and GO_CC.
demo result of seq2pathway function from chip seq data
data("dat_seq2pathway_Msig")data("dat_seq2pathway_Msig")
A list with 3 elements.
seq2gene_resulta list with 2 annotation table
gene2pathway_result.FAIMEa data frame of gene2pathway test result by MsigDB C5 terms
gene2pathway_result.FETa data frame of fisher's test resultby MsigDB C5 terms
A list, with three elements. The name of first element is seq2gene_result, with 2 data frames of full and coding gene annotation respectively, the second element is a data frame of "gene2pathway_result.FAIME", the third is a data frame of "gene2pathway_result.FET".
Description of GO term BP
data("Des_BP_list")data("Des_BP_list")
A list, list names are Go term BP's IDs, list elements are GO term BP's descritpion respectively.
A list, list names are Go term BP's IDs, list elements are GO term BP's descritpion respectively.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
data(Des_BP_list) head(names(Des_BP_list)) head(Des_BP_list)data(Des_BP_list) head(names(Des_BP_list)) head(Des_BP_list)
Description of GO term CC
data("Des_CC_list")data("Des_CC_list")
A list, list names are Go term CC's IDs, list elements are GO term CC's descritpion respectively.
A list, list names are Go term CC's IDs, list elements are GO term CC's descritpion respectively.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
data(Des_CC_list) head(names(Des_CC_list)) head(Des_CC_list)data(Des_CC_list) head(names(Des_CC_list)) head(Des_CC_list)
Description of GO term MF
data("Des_MF_list")data("Des_MF_list")
A list, list names are Go term MF's IDs, list elements are GO term MF's descritpion respectively.
A list, list names are Go term MF's IDs, list elements are GO term MF's descritpion respectively.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
data(Des_MF_list) head(names(Des_MF_list)) head(Des_MF_list)data(Des_MF_list) head(names(Des_MF_list)) head(Des_MF_list)
Coding gene list in GENCODE 20.
data("gencode_coding")data("gencode_coding")
A vector including all coding gene symbols in GENCODE version20.
A character vector including all coding gene symbols in GENCODE version20.
GENCODE 20
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project
data(gencode_coding) head(gencode_coding)data(gencode_coding) head(gencode_coding)
demo data of adding gene description
data("gene_description")data("gene_description")
A data frame with 561 observations on the following 2 variables.
hgnc_symbola characteristic vector
descriptiona characteristic vector
A characteristic matrix of gene symbols and descriptions.
Gene symbol list of GO term BP
data("GO_BP_list")data("GO_BP_list")
A list, list names are Go term BP's IDs, list elements are gene symbols in GO term BP.
A list, list names are Go term BP's IDs, list elements are gene symbols in GO term BP.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
data(GO_BP_list) head(GO_BP_list)data(GO_BP_list) head(GO_BP_list)
Gene symbol list of GO term CC
data("GO_CC_list")data("GO_CC_list")
A list, list names are Go term CC's IDs, list elements are gene symbols in GO term CC.
A list, list names are Go term CC's IDs, list elements are gene symbols in GO term CC.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
data(GO_CC_list) head(GO_CC_list)data(GO_CC_list) head(GO_CC_list)
intersection genes of GO terms and GENCODE 19
data("GO_GENCODE_df_hg_v19")data("GO_GENCODE_df_hg_v19")
A data frame.
A data frame.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project
data(GO_GENCODE_df_hg_v19) head(GO_GENCODE_df_hg_v19)data(GO_GENCODE_df_hg_v19) head(GO_GENCODE_df_hg_v19)
intersection genes of GO terms and GENCODE 36
data("GO_GENECODE_df_hg_v36")data("GO_GENECODE_df_hg_v36")
A data frame.
A data frame.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project
data(GO_GENECODE_df_hg_v36) head(GO_GENCODE_df_hg_v36)data(GO_GENECODE_df_hg_v36) head(GO_GENCODE_df_hg_v36)
intersection genes of GO terms and GENCODE vM1
data("GO_GENCODE_df_mm_vM1")data("GO_GENCODE_df_mm_vM1")
A data frame.
A data frame.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project
data(GO_GENCODE_df_mm_vM1) head(GO_GENCODE_df_mm_vM1)data(GO_GENCODE_df_mm_vM1) head(GO_GENCODE_df_mm_vM1)
intersection genes of GO terms and GENCODE vM25 simply by gene symbol match
data("GO_GENCODE_df_mm_vM25")data("GO_GENCODE_df_mm_vM25")
A data frame.
A data frame.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project
data(GO_GENECODE_df_mm_vM25) head(GO_GENCODE_df_mm_vM25)data(GO_GENECODE_df_mm_vM25) head(GO_GENCODE_df_mm_vM25)
Gene symbol list of GO term MF
data("GO_MF_list")data("GO_MF_list")
A list, list names are Go term MF's IDs, list elements are gene symbols in GO term MF.
A list, list names are Go term MF's IDs, list elements are gene symbols in GO term MF.
Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.0.0.
data(GO_MF_list) head(GO_MF_list)data(GO_MF_list) head(GO_MF_list)
intersection genes of MSigDB collection and GENCODE 19
data("Msig_GENCODE_df_hg_v19")data("Msig_GENCODE_df_hg_v19")
A data frame.
A data frame.
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project. Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550).
data(Msig_GENCODE_df_hg_v19) head(Msig_GENCODE_df_hg_v19)data(Msig_GENCODE_df_hg_v19) head(Msig_GENCODE_df_hg_v19)
intersection genes of MSigDB collection and GENCODE 36
data("Msig_GENCODE_df_hg_v36")data("Msig_GENCODE_df_hg_v36")
A data frame.
A data frame.
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project. Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550).
data(Msig_GENECODE_df_hg_v36) head(Msig_GENECODE_df)data(Msig_GENECODE_df_hg_v36) head(Msig_GENECODE_df)
intersection genes of MSigDB collection and GENCODE vM1
data("Msig_GENCODE_df_mm_vM1")data("Msig_GENCODE_df_mm_vM1")
A data frame.
A data frame.
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project. Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550).
data(Msig_GENCODE_df_mm_vM1) head(Msig_GENCODE_df_mm_vM1)data(Msig_GENCODE_df_mm_vM1) head(Msig_GENCODE_df_mm_vM1)
intersection genes of MSigDB collection and GENCODE vM25 simply by gene symbol match
data("Msig_GENCODE_df_mm_vM25")data("Msig_GENCODE_df_mm_vM25")
A data frame.
A data frame.
Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project. Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550).
data(Msig_GENECODE_df_mm_vM25) head(Msig_GENECODE_df)data(Msig_GENECODE_df_mm_vM25) head(Msig_GENECODE_df)
.gsa format data
data("MsigDB_C5")data("MsigDB_C5")
A list with 3 sub lists.
genesetsa list of gene names
geneset.namesa list of geneset names
geneset.descriptionsa list of geneset descriptions
A "GSA.genesets" object from GSA package.