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customprodb
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826
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
2.2 years ago
Esraa
• 0
0
votes
1
reply
839
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 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
Esraa
• 0
0
votes
0
replies
515
views
customProDB: error aberrant fasta from SNV
customProDB
2.6 years ago
finoa.li
• 0
0
votes
0
replies
751
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
3.0 years ago
04.marshal-decibel
• 0
0
votes
0
replies
1.1k
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
3.1 years ago
04.marshal-decibel
• 0
0
votes
1
reply
1.1k
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
5.8 years ago
laura.fancello
• 0
0
votes
1
reply
1.2k
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
6.1 years ago
Elena.M
• 0
4
votes
9
replies
4.4k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 15 months ago by
Yun
• 0 • written 6.5 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.2k
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 7.0 years ago by
xiaojing.wang
▴ 50 • written 7.0 years ago by
iranmdl15
• 0
0
votes
1
reply
1.3k
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 7.0 years ago by
xiaojing.wang
▴ 50 • written 7.2 years ago by
samupatt
• 0
0
votes
1
reply
1.3k
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 7.0 years ago by
xiaojing.wang
▴ 50 • written 7.4 years ago by
georges.bedran
• 0
0
votes
3
replies
2.1k
views
calculateRPKM error in customProDB
software error
customprodb
updated 3.7 years ago by
Anne
• 0 • written 8.1 years ago by
javamng
▴ 10
0
votes
0
replies
1.2k
views
Annotation package generation error for customprodb for hg38
customprodb
7.5 years ago
arunima2
• 0
1
vote
1
reply
1.7k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 3.7 years ago by
Anne
• 0 • written 8.1 years ago by
javamng
▴ 10
0
votes
1
reply
1.3k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 8.7 years ago by
xiaojing.wang
▴ 50 • written 8.7 years ago by
georges.bedran
• 0
0
votes
0
replies
1.4k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
9.0 years ago
yeh234
• 0
0
votes
1
reply
1.3k
views
CustomproDB JunctionType function
customprodb
updated 9.1 years ago by
xiaojing.wang
▴ 50 • written 9.1 years ago by
georges.bedran
• 0
0
votes
1
reply
1.4k
views
Pull request for customProDB package
customProDB
featurerequest
updated 9.3 years ago by
Dan Tenenbaum
★ 8.2k • written 9.3 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
2.3k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 10.1 years ago by
xiaojing.wang
▴ 50 • written 10.1 years ago by
kristenbeck527
• 0
2
votes
2
replies
2.0k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 10.1 years ago by
xiaojing.wang
▴ 50 • written 10.1 years ago by
kristenbeck527
• 0
2
votes
4
replies
2.1k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 10.1 years ago by
xiaojing.wang
▴ 50 • written 10.1 years ago by
kristenbeck527
• 0
21 results • Page
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Replies
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
ATpoint
★ 4.9k
No, cells from the same donor are correlated due to the donor effect. There is literature on this you should read to get started. https:/…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
Raya
• 0
Wouldn't each sample in the single cell rna seq act as a biological replicate? each condition (eg: mab3_20C) has ~70 single cell samples.
Comment: Getting way too many DEGs with LRT for time-series RNA-seq!
by
James W. MacDonald
68k
>Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! They are not the…
Comment: Getting way too many DEGs with LRT for time-series RNA-seq!
by
Denise
• 0
Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! And I suppose ther…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
ATpoint
★ 4.9k
There is no biological replication here. This is not supported by DESeq2 (or mos credible statistical tools). You would need different dono…
Votes
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Answer: Are voomByGroup and voomLmFit compatible?
Answer: p-adjusted values in multiple comparisons
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