User: knishida

gravatar for knishida
knishida20
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United States
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5 days, 23 hours ago
Joined:
3 years, 3 months ago
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k*******@riken.jp

Posts by knishida

<prev • 19 results • page 1 of 2 • next >
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Is there any annotation package for MSEA?
... I am considering submitting https://github.com/afukushima/MSEApdata as an annotation package of bioconductor. It seems that there is no data package (metabolite set for each function) for metabolite set enrichment analysis (MSEA) yet in bioconductor. Could you give me some advice on data packaging ...
metabolite data written 15 days ago by knishida20 • updated 14 days ago by shepherl ♦♦ 750
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Answer: A: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... I slightly update the repository like this https://github.com/kozo2/org.Slycopersicum.eg.db/commit/270527696df082246b05bf5f1544e7541414a909 Now there is an AnnotationDb object in my package. (and I can select the columns) > library(org.Slycopersicum.eg.db) > columns(org.Slycopersicum.eg.db) ...
written 2.6 years ago by knishida20
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Answer: A: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... I'm sorry I don't know why my posts were done redundantly. Could you please delete the duplicate posts? ...
written 2.6 years ago by knishida20
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Comment: C: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... The missing info is like this. LycoCyc pathway annotation The International Tomato Annotation Group (ITAG) ID Sol Genomics Network ID Uniprot ID I created the sqlite file with https://github.com/kozo2/org.Slycopersicum.eg.db-gen , and create the OrgDb with https://github.com/kozo2/org.Slyco ...
written 2.6 years ago by knishida20
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Comment: C: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... The missing info is like this. LycoCyc pathway annotation The International Tomato Annotation Group (ITAG) ID Sol Genomics Network ID Uniprot ID I created the sqlite file with https://github.com/kozo2/org.Slycopersicum.eg.db-gen , and create the OrgDb with https://github.com/kozo2/org.Slyco ...
written 2.6 years ago by knishida20
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Comment: C: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... The missing info is like this. LycoCyc pathway annotation The International Tomato Annotation Group (ITAG) ID Sol Genomics Network ID Uniprot ID I created the sqlite file with https://github.com/kozo2/org.Slycopersicum.eg.db-gen , and create the OrgDb with https://github.com/kozo2/org.Slyco ...
written 2.6 years ago by knishida20
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Answer: A: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... Thanks Guido I know the tomato OrgDb in AnnotationHub, but the OrgDb does not have some bimaps I need. (So I'm trying to create new one.) ...
written 2.6 years ago by knishida20
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ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
... Hi  I'm trying to create tomato orgdb at https://github.com/kozo2/org.Slycopersicum.eg.db It seems almost OK but the MAPCOUNTS is nil. Can I ask your comments or suggestions?   > install.packages("devtools") > devtools::install_github("kozo2/org.Slycopersicum.eg.db") > library("org.Sl ...
annotation orgdb written 2.6 years ago by knishida20
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Comment: C: Errors in makeOrgPackage
... Sorry, I forgot to add > biocLite("GO.db") to how to reproduce this error. ...
written 2.9 years ago by knishida20
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Comment: C: Errors in makeOrgPackage
... Many thanks for your advise. fUniprot was data.table as you indicated. I replaced it to data.frame it works well now. https://github.com/kozo2/org.Sl.eg.db/issues/1 ...
written 2.9 years ago by knishida20

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