Package: seq2pathway.data 1.44.0

Arjun Kinstlick

seq2pathway.data: data set for R package seq2pathway

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]>

# Install 'seq2pathway.data' in R:

install.packages('seq2pathway.data', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

dat_gene2path_chip - Demo result of gene2pathway function from chip seq data
dat_gene2path_RNA - Demo result of gene2pathway function from RNA seq data
dat_seq2pathway_GOterms - Demo result of seq2pathway function from chip seq data
dat_seq2pathway_Msig - Demo result of seq2pathway function from chip seq data
Des_BP_list - Description of GO term BP
Des_CC_list - Description of GO term CC
Des_MF_list - Description of GO term MF
gencode_coding - Coding gene list in GENCODE 20.
gene_description - Demo data of adding gene description
GO_BP_list - Gene symbol list of GO term BP
GO_CC_list - Gene symbol list of GO term CC
GO_GENCODE_df_hg_v19 - Intersection genes of GO terms and GENCODE 19
GO_GENCODE_df_mm_vM1 - Intersection genes of GO terms and GENCODE vM1
GO_MF_list - Gene symbol list of GO term MF
Msig_GENCODE_df_hg_v19 - Intersection genes of MSigDB collection and GENCODE 19
Msig_GENCODE_df_mm_vM1 - Intersection genes of MSigDB collection and GENCODE vM1
MsigDB_C5 - MsigDB data set

On BioConductor:seq2pathway.data-1.45.0(data/experiment 3.24)seq2pathway.data-1.44.0(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:2474cb1c05 (on RELEASE_3_23). Checks:1 ERROR, 2 WARNING, 1 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	ERROR	112
linux-devel	WARNING	220
source / vignettes	OK	258
linux-release	WARNING	202

Exports:

Dependencies:

An R data package for sequence

Last update: 2021-04-19
Started: 2021-03-26

Help page	Topics
demo result of gene2pathway function from chip seq data	dat_gene2path_chip
demo result of gene2pathway function from RNA seq data	dat_gene2path_RNA
demo result of seq2pathway function from chip seq data	dat_seq2pathway_GOterms
demo result of seq2pathway function from chip seq data	dat_seq2pathway_Msig
Description of GO term BP	Des_BP_list
Description of GO term CC	Des_CC_list
Description of GO term MF	Des_MF_list
Coding gene list in GENCODE 20.	gencode_coding
demo data of adding gene description	gene_description
Gene symbol list of GO term BP	GO_BP_list
Gene symbol list of GO term CC	GO_CC_list
intersection genes of GO terms and GENCODE 19	GO_GENCODE_df_hg_v19
intersection genes of GO terms and GENCODE 36	GO_GENCODE_df_hg_v36
intersection genes of GO terms and GENCODE vM1	GO_GENCODE_df_mm_vM1
intersection genes of GO terms and GENCODE vM25	GO_GENCODE_df_mm_vM25
Gene symbol list of GO term MF	GO_MF_list
intersection genes of MSigDB collection and GENCODE 19	Msig_GENCODE_df_hg_v19
intersection genes of MSigDB collection and GENCODE 36	Msig_GENCODE_df_hg_v36
intersection genes of MSigDB collection and GENCODE vM1	Msig_GENCODE_df_mm_vM1
intersection genes of MSigDB collection and GENCODE vM25	Msig_GENCODE_df_mm_vM25
MsigDB data set	MsigDB_C5