Showing : Rle • reset
2
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1
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1.7k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by ▴ 10
0
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1
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1.3k
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
0
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1
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2.2k
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RLE plot of DESeq2 normalisation / extract matrix of normalised counts from DESeqDataSet
deseq2 RLE
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
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2
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1.5k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 6.8 years ago by ★ 6.8k • written 6.8 years ago by • 0
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0
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1.2k
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Avoid rotating vector when doing arithmetic on different length IRanges RleList entries
iranges s4vectors rle rlelist
6.8 years ago endrebak85 ▴ 40
1
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1
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3.7k
views
What does the relative-log expression normalization mean in the deseq2 wrapper function ?
rle deseq2 normalization
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 20
1
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1
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1.4k
views
Subsetting Rle with ORF-sequence-positions by the 3 frames
Rle Big data coverageByTranscript
7.0 years ago hauken_heyken ▴ 80
7
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4
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1.9k
views
From RleList to RleArray
delayedarray rlelist rle
updated 7.4 years ago by ▴ 750 • written 7.4 years ago by ▴ 980
2
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4
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1.8k
views
Generic functions for DataFrames of Rle objects ?
DataFrame Rle generic expression table
updated 21 months ago by 16k • written 7.9 years ago by ▴ 180
0
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3
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2.0k
views
Efficiently construct GRanges/IRanges from Rle vector
Rle granges iranges
8.5 years ago my4 ▴ 10
0
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1
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1.9k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 170
6
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3
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3.2k
views
how does coverage() works
biostrings coverage rle iranges
8.9 years ago likeeatingpizza ▴ 10
0
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1
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1.6k
views
extract RLE normalized table
rle normalization table
updated 9.5 years ago by ★ 13k • written 9.5 years ago by • 0
3
votes
7
replies
2.4k
views
Add up RLEs that are in lists?
RLE GenomicFeatures rnaseq
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 30
2
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6
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3.1k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 30
2
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4
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2.3k
views
summing integer RLE
rle list irange grangeslist
updated 10.0 years ago by ▴ 80 • written 10.0 years ago by ▴ 30
1
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2
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1.4k
views
Summary statistics of RleListViews object
rle Views
10.1 years ago Sean Davis 21k
2
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5
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1.7k
views
making a RleViewsList object gets slow with many chromosomes
views iranges rle
10.2 years ago Janet Young ▴ 740
1
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1
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2.6k
views
Computing NUSE and RLE scores
affyPLM RLE NUSE
updated 10.2 years ago by 21k • written 10.2 years ago by ▴ 10
0
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2
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1.4k
views
boxplot on an Rle object?
Rle boxplot
10.2 years ago Johannes Rainer ★ 2.1k
20 results • Page 1 of 1
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Answer: fast apply on RleList by story.benjamin ▴ 20
solved with viewApply (code is simplified below) + map reduce on chrs test.split <- split(test.gr,seqnames(test.gr)) final.st…
Comment: fast apply on RleList by story.benjamin ▴ 20
Hi James, thanks for the reply. I ultimately figured it out ... viewApply showed a massive speed increase for me (see other answer) - I was…
Answer: fast apply on RleList by James W. MacDonald 68k
There is already a 'mean' function that will dispatch on an `RleList` that you can use. I don't have a long `RleList` in hand to test it on…
Answer: Custom CDF creation for HTA 2.0 array using GTF annotation by James W. MacDonald 68k
It doesn't appear that Manhong Dai is working at UM any longer, and the webpage appears to have fallen into disrepair (for example, the lin…
Comment: how to use `arrayWeightsQuick()`? by matthew • 0
In the specific use-case I have in mind, `expression` is a simple `matrix` of log2 gene expression per sample, no missing values.
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annotation EpicV2
Answer: fast apply on RleList
Answer: BiocParallel_1.40.1.tar.gz not available
Modelling gene program dynamics across time with {lemur}
A: DESeq2 one group vs multiple groups comparison in presence of batch effect
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