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customProDB
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437
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
464
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
284
views
customProDB: error aberrant fasta from SNV
customProDB
15 months ago
finoa.li
• 0
0
votes
0
replies
448
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
780
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
936
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
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
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
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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Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
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?
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