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customprodb
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521
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
12 months ago
Esraa
• 0
0
votes
1
reply
517
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 13 months ago by
James W. MacDonald
66k • written 13 months ago by
Esraa
• 0
0
votes
0
replies
312
views
customProDB: error aberrant fasta from SNV
customProDB
17 months ago
finoa.li
• 0
0
votes
0
replies
488
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
23 months ago
04.marshal-decibel
• 0
0
votes
0
replies
842
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
24 months ago
04.marshal-decibel
• 0
0
votes
1
reply
784
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
4.7 years ago
laura.fancello
• 0
0
votes
1
reply
877
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
5.0 years ago
Elena.M
• 0
4
votes
9
replies
3.3k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 6 weeks ago by
Yun
• 0 • written 5.3 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
964
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 5.8 years ago by
xiaojing.wang
▴ 50 • written 5.8 years ago by
iranmdl15
• 0
0
votes
1
reply
953
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 5.9 years ago by
xiaojing.wang
▴ 50 • written 6.0 years ago by
samupatt
• 0
0
votes
1
reply
973
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 5.9 years ago by
xiaojing.wang
▴ 50 • written 6.2 years ago by
georges.bedran
• 0
0
votes
3
replies
1.7k
views
calculateRPKM error in customProDB
software error
customprodb
updated 2.6 years ago by
Anne
• 0 • written 6.9 years ago by
javamng
▴ 10
0
votes
0
replies
948
views
Annotation package generation error for customprodb for hg38
customprodb
6.4 years ago
arunima2
• 0
1
vote
1
reply
1.5k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 2.6 years ago by
Anne
• 0 • written 6.9 years ago by
javamng
▴ 10
0
votes
1
reply
1.1k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 7.5 years ago by
xiaojing.wang
▴ 50 • written 7.6 years ago by
georges.bedran
• 0
0
votes
0
replies
1.2k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
7.9 years ago
yeh234
• 0
0
votes
1
reply
1.1k
views
CustomproDB JunctionType function
customprodb
updated 8.0 years ago by
xiaojing.wang
▴ 50 • written 8.0 years ago by
georges.bedran
• 0
0
votes
1
reply
1.1k
views
Pull request for customProDB package
customProDB
featurerequest
updated 8.1 years ago by
Dan Tenenbaum
★ 8.2k • written 8.1 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
1.9k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 9.0 years ago by
xiaojing.wang
▴ 50 • written 9.0 years ago by
kristenbeck527
• 0
2
votes
2
replies
1.7k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 9.0 years ago by
xiaojing.wang
▴ 50 • written 9.0 years ago by
kristenbeck527
• 0
2
votes
4
replies
1.8k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 9.0 years ago by
xiaojing.wang
▴ 50 • written 9.0 years ago by
kristenbeck527
• 0
21 results • Page
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Comment: Trouble Installing DADA2 (warning: R new user)
by
shepherl
3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Answer: LRT test for different timepoints (one tissue types vs. many tissue types)
by
Michael Love
42k
No, this is a contrast of estimated coefficient (e.g. the Wald test).
Comment: Ranking the GSEA Results
by
Michael Love
42k
Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…
Comment: Ranking the GSEA Results
by
V_Vibes
• 0
I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…
Comment: Ranking the GSEA Results
by
V_Vibes
• 0
The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…
Votes
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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