Showing : regioner • reset
6
votes
1
reply
1.8k
views
Retrieving Regions from hg38 of the same GC content and length with a list of elements
regioneR GRanges GCcontent
updated 8.4 years ago by ▴ 150 • written 8.4 years ago by ▴ 80
6
votes
5
replies
3.1k
views
Error running the function permTest
regioner overlappingpeaks
updated 7.0 years ago by ▴ 150 • written 7.0 years ago by ▴ 10
2
votes
5
replies
1.9k
views
permutation test on one set of data to get p-value of highest peaks. permTest? How?
regioneR permTest
6.1 years ago linuxborg2 • 0
2
votes
5
replies
1.3k
views
Sample code doesn't seem to be working on fresh install of regioneR
regioner
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 140
2
votes
1
reply
1.2k
views
Conflicting results in 'overlapPermTest' function from regioneR package
regioneR
updated 7.3 years ago by ▴ 150 • written 7.3 years ago by ▴ 40
2
votes
1
reply
1.2k
views
RegioneR perm test result Plot- how is y axis calculated
regioneR
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by ▴ 10
1
vote
1
reply
1.2k
views
Given a multifasta file and for each sequence, shuffle middle part of the sequence leaving the flanks intact and the opposite
shuffle regioner seqinr
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 80
1
vote
1
reply
643
views
regioneR meanInRegions to evaluate mutation accumulation
regioneR
updated 5.0 years ago by ▴ 150 • written 5.0 years ago by ▴ 40
0
votes
0
replies
650
views
overlapPermTest will not allow randomizing from MASKED hg19
regioner
5.8 years ago peds09 • 0
0
votes
1
reply
1.1k
views
sampling random regions of same nucleotide composition from hg38 genome
annotatr regioneR gkmSVM
updated 5 months ago by • 0 • written 3.3 years ago by ▴ 20
0
votes
1
reply
953
views
width(GRanges) increases after randomizeRegions(..) in package RegioneR
genomicranges regioneR width
updated 8.2 years ago by ▴ 150 • written 8.2 years ago by ▴ 40
0
votes
1
reply
1.3k
views
regioneR: error when verbose=TRUE
regioneR
updated 7.8 years ago by ▴ 30 • written 7.8 years ago by • 0
0
votes
0
replies
820
views
permTest plot Evobs bar moves and it should not
regioner permtest
6.1 years ago linuxborg2 • 0
0
votes
1
reply
649
views
Is localZScore function of regioneR mask-aware?
regioneR
updated 5.0 years ago by ▴ 150 • written 5.0 years ago by ▴ 40
0
votes
3
replies
883
views
Replacement error in PermTest
regioneR
4.8 years ago AlejandroMA • 0
0
votes
1
reply
671
views
behaviour of regioneR permTest function
regioneR
updated 4.6 years ago by ▴ 150 • written 4.6 years ago by • 0
0
votes
1
reply
877
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 3.5 years ago by ▴ 150 • written 3.9 years ago by • 0
17 results • Page 1 of 1
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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.
Comment: 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…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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