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customProDB
•
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0
votes
1
reply
435
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
10 months ago
Esraa
• 0
0
votes
1
reply
462
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 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Esraa
• 0
0
votes
0
replies
283
views
customProDB: error aberrant fasta from SNV
customProDB
15 months ago
finoa.li
• 0
0
votes
0
replies
447
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
20 months ago
04.marshal-decibel
• 0
0
votes
0
replies
779
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
21 months ago
04.marshal-decibel
• 0
0
votes
1
reply
747
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
4.5 years ago
laura.fancello
• 0
0
votes
1
reply
779
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
4.8 years ago
Elena.M
• 0
3
votes
8
replies
3.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
5.1 years ago
daniel.magnus.bader
▴ 40
0
votes
1
reply
923
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 5.6 years ago by
xiaojing.wang
▴ 50 • written 5.6 years ago by
iranmdl15
• 0
0
votes
1
reply
907
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 5.7 years ago by
xiaojing.wang
▴ 50 • written 5.8 years ago by
samupatt
• 0
0
votes
1
reply
935
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 5.7 years ago by
xiaojing.wang
▴ 50 • written 6.0 years ago by
georges.bedran
• 0
0
votes
0
replies
911
views
Annotation package generation error for customprodb for hg38
customprodb
6.2 years ago
arunima2
• 0
1
vote
1
reply
1.4k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 2.4 years ago by
Anne
• 0 • written 6.7 years ago by
javamng
▴ 10
0
votes
3
replies
1.7k
views
calculateRPKM error in customProDB
software error
customprodb
updated 2.4 years ago by
Anne
• 0 • written 6.7 years ago by
javamng
▴ 10
0
votes
1
reply
1.1k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 7.4 years ago by
xiaojing.wang
▴ 50 • written 7.4 years ago by
georges.bedran
• 0
0
votes
0
replies
1.1k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
7.7 years ago
yeh234
• 0
0
votes
1
reply
1.0k
views
CustomproDB JunctionType function
customprodb
updated 7.8 years ago by
xiaojing.wang
▴ 50 • written 7.8 years ago by
georges.bedran
• 0
0
votes
1
reply
1.1k
views
Pull request for customProDB package
customProDB
featurerequest
updated 7.9 years ago by
Dan Tenenbaum
★ 8.2k • written 7.9 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
1.8k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 8.8 years ago by
xiaojing.wang
▴ 50 • written 8.8 years ago by
kristenbeck527
• 0
2
votes
2
replies
1.6k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 8.8 years ago by
xiaojing.wang
▴ 50 • written 8.8 years ago by
kristenbeck527
• 0
2
votes
4
replies
1.7k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 8.8 years ago by
xiaojing.wang
▴ 50 • written 8.8 years ago by
kristenbeck527
• 0
21 results • Page
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Recent ...
Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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