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Rle
•
reset
1
vote
1
reply
985
views
deseq2 RLE normalization
RLE
normalization
deseq2
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
SH
• 0
0
votes
1
reply
841
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4
Rcpp
InteractionSet
IRanges
Rle
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
lklei001
• 0
0
votes
1
reply
1.7k
views
RLE plot of DESeq2 normalisation / extract matrix of normalised counts from DESeqDataSet
deseq2
RLE
updated 4.2 years ago by
Michael Love
41k • written 4.2 years ago by
f_pardow
• 0
0
votes
2
replies
1.2k
views
Error: invalid class "VRanges" object
variantannotation
VRanges
R
Rle
updated 5.9 years ago by
Valerie Obenchain
★ 6.8k • written 5.9 years ago by
Jayendra Shinde
• 0
0
votes
0
replies
968
views
Avoid rotating vector when doing arithmetic on different length IRanges RleList entries
iranges
s4vectors
rle
rlelist
5.9 years ago
endrebak85
▴ 40
1
vote
1
reply
3.0k
views
What does the relative-log expression normalization mean in the deseq2 wrapper function ?
rle
deseq2
normalization
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
Aurora
▴ 20
1
vote
1
reply
1.1k
views
Subsetting Rle with ORF-sequence-positions by the 3 frames
Rle
Big data
coverageByTranscript
6.0 years ago
hauken_heyken
▴ 80
7
votes
4
replies
1.6k
views
From RleList to RleArray
delayedarray
rlelist
rle
updated 6.5 years ago by
Peter Hickey
▴ 740 • written 6.5 years ago by
davide risso
▴ 950
2
votes
4
replies
1.4k
views
Generic functions for DataFrames of Rle objects ?
DataFrame
Rle
generic
expression table
updated 10 months ago by
Hervé Pagès
16k • written 6.9 years ago by
Charles Plessy
▴ 180
0
votes
3
replies
1.6k
views
Efficiently construct GRanges/IRanges from Rle vector
Rle
granges
iranges
7.6 years ago
my4
▴ 10
0
votes
1
reply
1.6k
views
Efficient coverage calculation with RleList and GRanges
granges
Rle
coverage
View
mean
updated 7.8 years ago by
Michael Lawrence
★ 11k • written 7.8 years ago by
Christian Ruckert
▴ 170
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings
coverage
rle
iranges
7.9 years ago
likeeatingpizza
▴ 10
0
votes
1
reply
1.4k
views
extract RLE normalized table
rle
normalization
table
updated 8.5 years ago by
Steve Lianoglou
★ 13k • written 8.5 years ago by
aiko
• 0
3
votes
7
replies
2.0k
views
Add up RLEs that are in lists?
RLE
GenomicFeatures
rnaseq
updated 9.1 years ago by
Hervé Pagès
16k • written 9.1 years ago by
gen
▴ 30
2
votes
6
replies
2.8k
views
Shrink or Expand RLE
RLE
iranges
granges
coverage
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
gen
▴ 30
2
votes
4
replies
1.9k
views
summing integer RLE
rle
list
irange
grangeslist
updated 9.1 years ago by
Chris Seidel
▴ 80 • written 9.1 years ago by
gen
▴ 30
1
vote
2
replies
1.1k
views
Summary statistics of RleListViews object
rle
Views
9.2 years ago
Sean Davis
21k
2
votes
5
replies
1.5k
views
making a RleViewsList object gets slow with many chromosomes
views
iranges
rle
9.2 years ago
Janet Young
▴ 740
1
vote
1
reply
2.3k
views
Computing NUSE and RLE scores
affyPLM
RLE
NUSE
updated 9.2 years ago by
Sean Davis
21k • written 9.2 years ago by
beverly893
▴ 10
0
votes
2
replies
1.2k
views
boxplot on an Rle object?
Rle
boxplot
9.3 years ago
Johannes Rainer
★ 2.0k
20 results • Page
1 of 1
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Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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