Showing : S4Vectors • reset
11
votes
17
replies
2.2k
views
SV4Vectors DataFrame bug with haven_labelled data
S4Vectors DataFrame haven_labelled haven
updated 16 months ago by ▴ 20 • written 16 months ago by ▴ 30
0
votes
15
replies
2.0k
views
Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
bioconductor iranges s4vectors xvector r 3.3.2
updated 5.7 years ago by ▴ 10 • written 5.7 years ago by • 0
3
votes
12
replies
2.5k
views
Trouble installing GOSemSim
GOSemSim S4Vectors
5.1 years ago sergi.picart ▴ 20
3
votes
12
replies
2.0k
views
S4Vectors and subectHits error
s4vectors copywriter
updated 6.0 years ago by ★ 11k • written 6.0 years ago by ▴ 200
1
vote
11
replies
1.7k
views
Error uploading deseq2
deseq2 S4Vectors
updated 4.0 years ago by 25k • written 4.0 years ago by • 0
5
votes
10
replies
2.1k
views
caught segfault error when loading S4Vectors package in R
R S4Vectors segfault
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 20
10
votes
10
replies
2.4k
views
Does package S4Vectors break ifelse?
S4Vectors ifelse
updated 6.8 years ago by ▴ 40 • written 8.7 years ago by ★ 3.0k
4
votes
10
replies
2.2k
views
Printing DataFrame with nested DataFrames causes error
s4vectors dataframe
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 70
2
votes
9
replies
1.7k
views
S4Vectors not loading
S4Vectors
4.1 years ago Panos Balomenos • 0
3
votes
8
replies
2.5k
views
S4Vectors masks/breaks regular Matrix functions
S4Vectors Matrix
7.2 years ago peter.kharchenko ▴ 30
0
votes
7
replies
3.2k
views
GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
4.5 years ago james.dalgleish ▴ 30
1
vote
7
replies
2.2k
views
What to do when all the installation methods for a package fail (pagoo)?
S4Vectors pagoo
22 months ago MauriAndres • 0
0
votes
6
replies
1.5k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
0
votes
6
replies
1.8k
views
Problem installing S4Vectors on Mac Mini M1 Big Sur
S4Vectors
2.5 years ago Richard • 0
5
votes
6
replies
617
views
DataFrame Construction With Non-standard Column
S4Vectors
updated 6 months ago by 16k • written 6 months ago by ★ 1.5k
4
votes
6
replies
1.5k
views
breakTies for a Hits-object based on value in mcols?
s4vectors hits
updated 6.3 years ago by ★ 11k • written 6.3 years ago by ▴ 170
5
votes
5
replies
1.4k
views
How to extract out wanted IntegerList more elegantly from nested list?
r s4vectors integerlist iranges
updated 7.6 years ago by ★ 11k • written 7.6 years ago by • 0
3
votes
5
replies
1.7k
views
How can I coerce "list" to S4 "List" (reproducible example is available)?
coercion data manipulation s4vectors List
7.8 years ago Jurat Shahidin ▴ 80
0
votes
5
replies
1.6k
views
Using S4Vectors within a package
Package s4vectors
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 10
0
votes
4
replies
1.7k
views
Unexpected behaviour of set operations on GRanges objects when dplyr is loaded
GenomicRanges S4Vectors dplyr
updated 5.3 years ago by 65k • written 5.3 years ago by ▴ 140
4
votes
4
replies
1.1k
views
S4Vectors masking utils::findMatches is returning warnings in R 4.3 / Bioconductor 3.17
S4Vectors
written 11 months ago by ▴ 90
1
vote
4
replies
1.7k
views
IRanges missing S4Vectors_defines.h
iranges s4vectors
updated 9.0 years ago by 16k • written 9.0 years ago by ▴ 10
0
votes
4
replies
1.6k
views
‘parallel_slot_names’ is not exported by 'namespace:S4Vectors'
S4Vectors
updated 3.3 years ago by 16k • written 3.3 years ago by • 0
1
vote
4
replies
2.5k
views
biocLite updating problem with Ubuntu 17.10
ubuntu biocgenerics s4vectors IRanges annotationdbi
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
5
votes
3
replies
3.7k
views
Add new columns to DESeqResults from text file by matching rownames.
deseq2 deseq merge data frames cbind s4vectors
updated 6.5 years ago by 41k • written 6.6 years ago by ▴ 10
2
votes
3
replies
910
views
S4Vectors, strange metadata behavior
GRangesList S4Vectors
updated 2.4 years ago by 16k • written 2.4 years ago by ▴ 80
0
votes
3
replies
1.3k
views
How can i fix this problem in R
S4Vectors DESeq2
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
2
votes
3
replies
1.5k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
8.2 years ago liz.ingsimmons ▴ 140
2
votes
3
replies
1.5k
views
"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
GenomicRanges rtracklayer VariantAnnotation S4Vectors SummarizedExperiment
updated 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 30
1
vote
3
replies
1.6k
views
Correct way to split and unsplit a DataFrame
s4vectors iranges
updated 4.7 years ago by ★ 11k • written 4.7 years ago by ▴ 90
0
votes
2
replies
515
views
Using dplyr commands with DataFrame objects
S4Vectors
6 months ago GE • 0
1
vote
2
replies
1.4k
views
Error running table() on an RleList returned by coverage()
GenomicRanges S4Vectors
updated 9.5 years ago by 16k • written 9.5 years ago by ★ 5.1k
1
vote
2
replies
3.3k
views
Error in installation S4Vectors package
s4vectors
updated 8.4 years ago by ★ 8.2k • written 8.4 years ago by • 0
2
votes
2
replies
2.1k
views
Problem when installing DESeq on MAC OS X
s4vectors mac os x deseq
updated 8.2 years ago by ★ 13k • written 8.2 years ago by • 0
1
vote
2
replies
1.7k
views
Installation problem, S4Vectors, something about "apply_hotfix73465" not found
package installation s4vectors
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
2
votes
2
replies
2.0k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
0
votes
2
replies
1.2k
views
DataFrame matrix subsetting
DataFrame subsetting S4Vectors
updated 5.3 years ago by 16k • written 5.3 years ago by • 0
5
votes
2
replies
902
views
DataFrame after splitting and back
DataFrame S4Vectors
updated 5.0 years ago by ★ 11k • written 5.0 years ago by 1.6k
0
votes
2
replies
1.3k
views
S4Vectors (and others) install error
s4vectors
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
3
votes
2
replies
2.5k
views
Convert DataFrame to data.frame While Keeping Column Name Syntax
S4Vectors
updated 2.9 years ago by 65k • written 2.9 years ago by ★ 1.5k
3
votes
2
replies
1.6k
views
Proper way to read in a DataFrame with CharacterList columns that was saved to a text file
s4vectors genomicranges
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ★ 1.0k
0
votes
1
reply
3.2k
views
problem in loading Deseq2
deseq2 S4Vectors
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
1
vote
1
reply
788
views
Checking if to DataFrames are identical
S4Vectors DataFrame
4.6 years ago maltethodberg ▴ 170
0
votes
1
reply
751
views
Why does S4Vectors define three functions for Vector -> data.frame coercion
S4Vectors methods
4.6 years ago Aditya ▴ 160
2
votes
1
reply
875
views
Adding a column to a class that contains DataFrame
s4vectors
6.3 years ago Michael Love 41k
2
votes
1
reply
844
views
DataFrame or DFrame
S4Vectors
updated 2.9 years ago by 690 • written 2.9 years ago by ★ 1.5k
0
votes
1
reply
1.4k
views
Is S4Vectors not able to install in R-3.5.1?
S4Vectors R-3.5.1
5.3 years ago zhang303 • 0
0
votes
1
reply
1.7k
views
RnBeads: Error in as.list.default(data.source) : no method for coercing this S4 class to a vector
rnbeads error as.vector(data) s4vectors s4
8.6 years ago schasse • 0
2
votes
1
reply
254
views
DataFrame Printing User Control
S4Vectors
updated 4 months ago by 16k • written 4 months ago by ★ 1.5k
1
vote
1
reply
948
views
Bug report: unpredictable coloumn ranaming in DataFrame class
S4Vectors
updated 7.0 years ago by ★ 11k • written 7.0 years ago by • 0
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Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Answer: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
The genes are automatically ordered within `fgsea`, there is no need to sort them manually.
Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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