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customProDB
•
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0
votes
1
reply
730
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
21 months ago
Esraa
• 0
0
votes
1
reply
736
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 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Esraa
• 0
0
votes
0
replies
446
views
customProDB: error aberrant fasta from SNV
customProDB
2.1 years ago
finoa.li
• 0
0
votes
0
replies
652
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
2.6 years ago
04.marshal-decibel
• 0
0
votes
0
replies
1.0k
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
2.7 years ago
04.marshal-decibel
• 0
0
votes
1
reply
957
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
5.3 years ago
laura.fancello
• 0
0
votes
1
reply
1.1k
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
5.6 years ago
Elena.M
• 0
4
votes
9
replies
4.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 9 months ago by
Yun
• 0 • written 6.0 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.2k
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 6.5 years ago by
xiaojing.wang
▴ 50 • written 6.5 years ago by
iranmdl15
• 0
0
votes
1
reply
1.2k
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 6.6 years ago by
xiaojing.wang
▴ 50 • written 6.7 years ago by
samupatt
• 0
0
votes
1
reply
1.2k
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 6.6 years ago by
xiaojing.wang
▴ 50 • written 6.9 years ago by
georges.bedran
• 0
0
votes
3
replies
2.0k
views
calculateRPKM error in customProDB
software error
customprodb
updated 3.3 years ago by
Anne
• 0 • written 7.6 years ago by
javamng
▴ 10
0
votes
0
replies
1.1k
views
Annotation package generation error for customprodb for hg38
customprodb
7.1 years ago
arunima2
• 0
1
vote
1
reply
1.6k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 3.3 years ago by
Anne
• 0 • written 7.6 years ago by
javamng
▴ 10
0
votes
1
reply
1.2k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 8.2 years ago by
xiaojing.wang
▴ 50 • written 8.2 years ago by
georges.bedran
• 0
0
votes
0
replies
1.3k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
8.6 years ago
yeh234
• 0
0
votes
1
reply
1.3k
views
CustomproDB JunctionType function
customprodb
updated 8.7 years ago by
xiaojing.wang
▴ 50 • written 8.7 years ago by
georges.bedran
• 0
0
votes
1
reply
1.3k
views
Pull request for customProDB package
customProDB
featurerequest
updated 8.8 years ago by
Dan Tenenbaum
★ 8.2k • written 8.8 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
2.2k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 9.7 years ago by
xiaojing.wang
▴ 50 • written 9.7 years ago by
kristenbeck527
• 0
2
votes
2
replies
1.9k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 9.7 years ago by
xiaojing.wang
▴ 50 • written 9.7 years ago by
kristenbeck527
• 0
2
votes
4
replies
2.0k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 9.7 years ago by
xiaojing.wang
▴ 50 • written 9.7 years ago by
kristenbeck527
• 0
21 results • Page
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Comment: Use of limma R package with targeted proteomics for DE analysis
by
svlachavas
▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Votes
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
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