Showing : variantannotation • reset
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5.1k
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merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 10.3 years ago by ★ 6.8k
0
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2
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3.5k
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VariantAnnotation R Package - Merging Two VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 9.3 years ago by ▴ 320
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2
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2.1k
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merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 10.4 years ago by ▴ 840
0
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1
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609
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Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 7 months ago by 63k • written 7 months ago by ▴ 10
4
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8
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476
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TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation
11 weeks ago davidhillis • 0
2
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4
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445
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Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
8 months ago rwan.work • 0
0
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3
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364
views
Add GP values to VCF
VariantAnnotation
5 months ago • updated 4 months ago Stephanie M. Gogarten ▴ 840
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2
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289
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Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
8 months ago rwan.work • 0
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0
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189
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
3 months ago therealgenna • 0
0
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2
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136
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 26 days ago by ★ 2.9k • written 26 days ago by • 0
10 results • Page 1 of 1
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Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k
See above, you want the sites where `Fold > 0`.
Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k
That does seem like you have a very high number of open chromatin sites changing. How many are in the consensus matrix? You can see how ma…
Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k
I can see the confusion here as one color is being used in two different ways. The dark blue/purple color is used for the bars on the left…
Comment: P-value histogram of testLinearModel is not uniform by ATpoint ★ 2.9k
The work from @csoneson (https://pubmed.ncbi.nlm.nih.gov/29481549/) points out that for scRNA-seq a good prefiltering improves DE reliabili…
Answer: Diffbind "No genome detected" by Rory Stark ★ 4.9k
In this case, `DiffBind` is unable to automatically determine the genome from the supplied Input bam file. You should be able to specify `g…
Votes
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Answer: P-value histogram of testLinearModel is not uniform
Answer: Interpret plot from DiffBind
C: Minimum number of samples per treatment/group for WGCNA analysis
Awards • All
Popular Question to rodrigo.duarte88 ▴ 30
Scholar to Rory Stark ★ 4.9k
Popular Question to arfranco ▴ 130
Popular Question to Johannes Rainer ★ 2.0k
Popular Question to Jenn ▴ 30
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