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VariantFiltering
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library VaraintFiltration looking for explanation of pedigree file
bioconductor
variantfiltering
6.7 years ago
Claus.Hultschig
• 0
0
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1
reply
345
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VariantFiltering error
VariantFiltering
updated 10 months ago by
Robert Castelo
★ 3.3k • written 10 months ago by
Andrew Beggs
▴ 90
3
votes
2
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1.4k
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filtering VCF files
variantannotation
variantfiltering
updated 7.1 years ago by
Michael Lawrence
★ 11k • written 7.1 years ago by
Bogdan
▴ 670
0
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1
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1.5k
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Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Mohamed
▴ 30
1
vote
1
reply
1.3k
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retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsistency
variantfiltering
phastcons
updated 9.0 years ago by
Robert Castelo
★ 3.3k • written 9.0 years ago by
Stefanie Tauber
▴ 40
0
votes
0
replies
1.7k
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problems installing VariantFiltering package
VariantFiltering
VariantFiltering
9.9 years ago
Robert Castelo
★ 3.3k
4
votes
0
replies
1.5k
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News:
Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing
transcription
variantfiltering
annotation
News
8.9 years ago
Matthew Ritchie
▴ 1000
0
votes
1
reply
1.1k
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Problems with autosomalRecessiveHomozygous
VariantFiltering
8.8 years ago
claire.simpson
• 0
0
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0
replies
438
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
7 months ago
Bogdan
▴ 670
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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