User: knishida

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knishida10
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New User
Location:
United States
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1 year, 9 months ago
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2 years, 5 months ago
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k*******@riken.jp

Posts by knishida

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Answer: A: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... I slightly update the repository like this https://github.com/kozo2/org.Slycopersicum.eg.db/commit/270527696df082246b05bf5f1544e7541414a909 Now there is an AnnotationDb object in my package. (and I can select the columns) > library(org.Slycopersicum.eg.db) > columns(org.Slycopersicum.eg.db) ...
written 21 months ago by knishida10
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Answer: A: ann_objs$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 21 months ago by knishida10
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Comment: C: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... The missing info is like this. LycoCyc pathway annotation The International Tomato Annotation Group (ITAG) ID Sol Genomics Network ID Uniprot ID I created the sqlite file with https://github.com/kozo2/org.Slycopersicum.eg.db-gen , and create the OrgDb with https://github.com/kozo2/org.Slyco ...
written 21 months ago by knishida10
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Comment: C: ann_objs$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 21 months ago by knishida10
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Comment: C: ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not w
... The missing info is like this. LycoCyc pathway annotation The International Tomato Annotation Group (ITAG) ID Sol Genomics Network ID Uniprot ID I created the sqlite file with https://github.com/kozo2/org.Slycopersicum.eg.db-gen , and create the OrgDb with https://github.com/kozo2/org.Slyco ...
written 21 months ago by knishida10
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Answer: A: ann_objs$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 21 months ago by knishida10
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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 21 months ago by knishida10
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Comment: C: Errors in makeOrgPackage
... Sorry, I forgot to add > biocLite("GO.db") to how to reproduce this error. ...
written 2.1 years ago by knishida10
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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 2.1 years ago by knishida10
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Errors in makeOrgPackage
... I'm trying to create a custom OrgDb for tomato. First I tried to add Uniprot table to the OrgDb with  https://github.com/kozo2/org.Sl.eg.db/blob/master/tomatoMakeOrgPkg.R but I had an error like https://gist.github.com/kozo2/528856852e372d74e429 May I ask for any advice? I checked this error o ...
annotation error written 2.1 years ago by knishida10 • updated 2.1 years ago by James W. MacDonald45k

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