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customprodb
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676
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customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
18 months ago
Esraa
• 0
0
votes
1
reply
667
views
Calculate RPKMs and Output proteins pass the cutoff into FASTA file ... Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : i…
customProDB
easyrun
error
mm10
Mus_musculus_Data
updated 19 months ago by
James W. MacDonald
67k • written 19 months ago by
Esraa
• 0
0
votes
0
replies
411
views
customProDB: error aberrant fasta from SNV
customProDB
22 months ago
finoa.li
• 0
0
votes
0
replies
607
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
2.4 years ago
04.marshal-decibel
• 0
0
votes
0
replies
984
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
2.4 years ago
04.marshal-decibel
• 0
0
votes
1
reply
910
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
5.1 years ago
laura.fancello
• 0
0
votes
1
reply
1.0k
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
5.4 years ago
Elena.M
• 0
4
votes
9
replies
3.8k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 7 months ago by
Yun
• 0 • written 5.8 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.1k
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 6.3 years ago by
xiaojing.wang
▴ 50 • written 6.3 years ago by
iranmdl15
• 0
0
votes
1
reply
1.1k
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 6.4 years ago by
xiaojing.wang
▴ 50 • written 6.5 years ago by
samupatt
• 0
0
votes
1
reply
1.1k
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 6.4 years ago by
xiaojing.wang
▴ 50 • written 6.7 years ago by
georges.bedran
• 0
0
votes
3
replies
1.9k
views
calculateRPKM error in customProDB
software error
customprodb
updated 3.0 years ago by
Anne
• 0 • written 7.4 years ago by
javamng
▴ 10
0
votes
0
replies
1.1k
views
Annotation package generation error for customprodb for hg38
customprodb
6.9 years ago
arunima2
• 0
1
vote
1
reply
1.6k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 3.0 years ago by
Anne
• 0 • written 7.4 years ago by
javamng
▴ 10
0
votes
1
reply
1.2k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 8.0 years ago by
xiaojing.wang
▴ 50 • written 8.0 years ago by
georges.bedran
• 0
0
votes
0
replies
1.3k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
8.3 years ago
yeh234
• 0
0
votes
1
reply
1.2k
views
CustomproDB JunctionType function
customprodb
updated 8.5 years ago by
xiaojing.wang
▴ 50 • written 8.5 years ago by
georges.bedran
• 0
0
votes
1
reply
1.2k
views
Pull request for customProDB package
customProDB
featurerequest
updated 8.6 years ago by
Dan Tenenbaum
★ 8.2k • written 8.6 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
2.1k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 9.4 years ago by
xiaojing.wang
▴ 50 • written 9.4 years ago by
kristenbeck527
• 0
2
votes
2
replies
1.8k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 9.5 years ago by
xiaojing.wang
▴ 50 • written 9.5 years ago by
kristenbeck527
• 0
2
votes
4
replies
1.9k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 9.5 years ago by
xiaojing.wang
▴ 50 • written 9.5 years ago by
kristenbeck527
• 0
21 results • Page
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Recent ...
Replies
Answer: Error in get_anno_data(ontology) : ontology not supported yet...
by
Guido Hooiveld
★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Comment: Build error on kunpeng2 Linux aarch64
by
martin.grigorov
▴ 10
Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…
Answer: Standardization of rlog transformed counts before PCA
by
ATpoint
★ 4.6k
I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Tim Peters
▴ 200
Also, re DMR.plot(), yes the understanding is that all DMRs from EPICv2 should be plotted in hg38. I've left that implied for the user sinc…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Tim Peters
▴ 200
Hi Xiaofei, Thanks for this. If your data is from 450K, you'll have to call your DMRs in hg19, and then lift the DMR ranges over to hg38 p…
Votes
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
Answer: Deseq2 Design
Answer: Fold change calculation in Diffbind vs. DESEQ2?
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