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customprodb
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471
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customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
11 months ago
Esraa
• 0
0
votes
1
reply
490
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 12 months ago by
James W. MacDonald
66k • written 12 months ago by
Esraa
• 0
0
votes
0
replies
296
views
customProDB: error aberrant fasta from SNV
customProDB
15 months ago
finoa.li
• 0
0
votes
0
replies
463
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
21 months ago
04.marshal-decibel
• 0
0
votes
0
replies
808
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
22 months ago
04.marshal-decibel
• 0
0
votes
1
reply
764
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
4.5 years ago
laura.fancello
• 0
0
votes
1
reply
814
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
4.9 years ago
Elena.M
• 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 7 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
939
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 5.7 years ago by
xiaojing.wang
▴ 50 • written 5.7 years ago by
iranmdl15
• 0
0
votes
1
reply
925
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 5.8 years ago by
xiaojing.wang
▴ 50 • written 5.9 years ago by
samupatt
• 0
0
votes
1
reply
950
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 5.8 years ago by
xiaojing.wang
▴ 50 • written 6.1 years ago by
georges.bedran
• 0
0
votes
3
replies
1.7k
views
calculateRPKM error in customProDB
software error
customprodb
updated 2.5 years ago by
Anne
• 0 • written 6.8 years ago by
javamng
▴ 10
0
votes
0
replies
928
views
Annotation package generation error for customprodb for hg38
customprodb
6.3 years ago
arunima2
• 0
1
vote
1
reply
1.5k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 2.5 years ago by
Anne
• 0 • written 6.8 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 7.5 years ago by
georges.bedran
• 0
0
votes
0
replies
1.1k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
7.8 years ago
yeh234
• 0
0
votes
1
reply
1.1k
views
CustomproDB JunctionType function
customprodb
updated 7.9 years ago by
xiaojing.wang
▴ 50 • written 7.9 years ago by
georges.bedran
• 0
0
votes
1
reply
1.1k
views
Pull request for customProDB package
customProDB
featurerequest
updated 8.0 years ago by
Dan Tenenbaum
★ 8.2k • written 8.0 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
1.9k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 8.9 years ago by
xiaojing.wang
▴ 50 • written 8.9 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 8.9 years ago by
xiaojing.wang
▴ 50 • written 8.9 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 8.9 years ago by
xiaojing.wang
▴ 50 • written 8.9 years ago by
kristenbeck527
• 0
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Comment: Slightly different count plots from R and spreadsheet
by
Michael Love
42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM
by
Vitor
• 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). …
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by
James W. MacDonald
66k
If you have beta values, try the `DSS` package. An alternative is to compute the logit transform (to M-values), which are amenable to analy…
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James W. MacDonald
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The obvious would be to check that you have genes that map to that pathway. It's unusual to have so many NA values for your NCBI gene IDs, …
Comment: ChAMP installation issue
by
Tahirah
• 0
Thanks a lot. But unfortunately it didn't work. I guess I will have to wait until ChAMP becomes available for version 3.19 In the meantime …
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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