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3
votes
6
replies
2.8k
views
Standardizing gene symbols
R
updated 7.9 years ago by 53k • written 7.9 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Solve overlapping gene labels in volcano plot when using textxy
R
7.9 years ago Nithisha ▴ 10
5
votes
2
replies
2.5k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Error installing flowDensity on latest docker container
R package installation docker
updated 7.9 years ago by 4.2k • written 7.9 years ago by • 0
1
vote
2
replies
2.0k
views
Package won't recognise raw data files
camera metabolomics r
7.9 years ago bhgyu ▴ 30
0
votes
12
replies
2.4k
views
DESeq2 different versions
rnaseq r deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
1
reply
1.7k
views
rhdf5 h5ls output differs from Linux to Windows
R h5ls windows linux
updated 7.9 years ago by ★ 6.6k • written 8.0 years ago by • 0
1
vote
1
reply
1.9k
views
Error in Rnbeads:Error in logger.error(em) : Could not create file. cannot popen '/usr/bin/which 'gs' 2>/dev/null', probable reason 'Cannot alloca…
R bioconductor rnbeads microarray illimina 450k methylation
7.9 years ago preethibagopi28 ▴ 10
1
vote
3
replies
2.0k
views
Pathway analysis from list of differentially expressed genes with fold change, pvalues and normalised expression levels in R
rnaseq pathway analysis R limma
updated 7.9 years ago by ▴ 760 • written 7.9 years ago by • 0
1
vote
2
replies
1.5k
views
R packages old versions
R deseq2 package
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
3
votes
3
replies
3.0k
views
Using sluth with Salmon data, error while sleuth_prep
sleuth R salmon rna seq salmon
7.9 years ago Walter F. Baumann ▴ 10
0
votes
3
replies
3.2k
views
warning: example doesn't exist; while trying to build a package
bioconductor package development R roxygen2 warning
8.0 years ago • updated 7.9 years ago clarisbaby • 0
0
votes
1
reply
2.4k
views
How to name the custom genome in karyoploteR ?
software error R bsgenome karyoploter
updated 7.9 years ago by ▴ 150 • written 8.0 years ago by ▴ 20
0
votes
1
reply
1.1k
views
How to take mean from specific column
Mean R
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 10
0
votes
1
reply
2.2k
views
How to install a bioconductor package RMySQL and specify R parameters
software error R
updated 8.0 years ago by 4.2k • written 8.0 years ago by ▴ 10
1
vote
8
replies
7.3k
views
Cannot read Biom file
r biomformat phyloseq
updated 8.0 years ago by ★ 1.1k • written 8.0 years ago by • 0
1
vote
1
reply
2.7k
views
Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts
updated 8.0 years ago by ▴ 160 • written 8.0 years ago by ▴ 10
0
votes
1
reply
1.2k
views
problem in installing IlluminaHumanMethylationEPICanno.ilm10b2.hg19
R software error package installation
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
1
vote
1
reply
1.6k
views
reading ped error when using the snpStats library
snpstats ped file R
8.0 years ago kzelaya2 ▴ 10
3
votes
4
replies
7.3k
views
Subset GRanges object into new object
R genomicranges subsetting
8.0 years ago jhanks1981 • 0
1
vote
5
replies
3.9k
views
'names' attribute [12] must be the same length as the vector [6]
R xcms vector
8.0 years ago bhgyu ▴ 30
3
votes
5
replies
6.7k
views
SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
R bioconductor singlecellexperiment single cell
updated 8.0 years ago by • 0 • written 8.0 years ago by ▴ 10
0
votes
2
replies
2.6k
views
error in library(clusterProfiler)
R
updated 8.0 years ago by • 0 • written 8.3 years ago by • 0
0
votes
2
replies
1.0k
views
Error in binning bam files
R makeBinnedCountsFile GenomicRanges
8.0 years ago greeshmathulasi1 • 0
0
votes
4
replies
4.9k
views
DESeq failure after update: unable to find an inherited method for function mcols for signature Rle
deseq2 deseq r version compatibility
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
votes
1
reply
1.7k
views
DEXSeq Count files do not correspond to the flattened annotation file
dexseq R
8.0 years ago firestar ▴ 20
0
votes
3
replies
2.8k
views
R Gviz ideogram custom track
Gviz ideogram track custom genome R
8.0 years ago wd ▴ 30
0
votes
0
replies
963
views
read.pedfile( ) error
R ped file
8.0 years ago kzelaya2 ▴ 10
3
votes
0
replies
2.0k
views
What's the correct way to normalize HTseq files with TCGAbiolinks
normalization R rnaseq bioconductor
8.0 years ago eshelden ▴ 40
0
votes
1
reply
1.6k
views
BioQC R package issue with broad gmt files
R BioQC gmt GSEA
8.0 years ago Seymoo • 0
1
vote
3
replies
1.8k
views
How to normalize Microarray expression data?
r affymetrix microarrays normalization bioconductor
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 120
1
vote
3
replies
2.5k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 22 months ago by ★ 5.2k • written 8.0 years ago by • 0
0
votes
0
replies
993
views
RobustRankAggreg in R
R
8.1 years ago lily ▴ 20
0
votes
3
replies
736
views
DESeq2 Which gene used to normalize?
deseq2 normalization R
updated 8.1 years ago by ★ 13k • written 8.1 years ago by • 0
1
vote
1
reply
12k
views
Pheatmap clustering and row annotation
R pheatmap cutree
8.1 years ago meseretbrihanu ▴ 10
0
votes
5
replies
1.0k
views
paired design with continious covariate
deseq2 r
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
1
vote
1
reply
3.3k
views
DiffBind broad and narrow peak identification
diffbind r chipseq
updated 8.1 years ago by ★ 5.2k • written 8.1 years ago by • 0
2
votes
3
replies
2.8k
views
MA plot DiffBind in ggplot2
diffbind ggplot2 r chipseq
updated 8.1 years ago by ★ 5.2k • written 8.1 years ago by • 0
0
votes
1
reply
1.6k
views
What R version does systemPipeR runs
systempiper R batchjobs
updated 8.1 years ago by ★ 1.7k • written 8.1 years ago by • 0
0
votes
6
replies
1.8k
views
DEXSeq error with estimateExonFoldChanges
software error dexseq R
8.1 years ago Chen • 0
2
votes
0
replies
1.3k
views
p-values, q-values, duplicated entries in output - ballgown
ballgown rna-seq q value r
8.1 years ago mkhasin ▴ 20
0
votes
19
replies
2.8k
views
Paired Difference Analysis
deseq2 R differential gene expression
8.2 years ago • updated 8.1 years ago nhua • 0
4
votes
1
reply
2.4k
views
Retrieving all genes related a go term
go R annotationdbi biomart
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 40
2
votes
3
replies
1.1k
views
interaction between continious and categorical variables
deseq2 r
8.1 years ago fabian.roger • 0
1
vote
5
replies
3.3k
views
Get cytoband from refsnp ID using biomaRt in R
biomart R
updated 8.1 years ago by ★ 6.6k • written 8.1 years ago by ▴ 20
2
votes
10
replies
2.8k
views
DiffBind consensus peak help
diffbind r chipseq
updated 8.1 years ago by ★ 5.2k • written 8.1 years ago by • 0
2
votes
2
replies
1.7k
views
Solving error for error of factors
deseq2 cancer R
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 30
0
votes
2
replies
733
views
R script problem
R rnaseq bioconductor
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
0
votes
2
replies
1.6k
views
diffbind Error: cannot allocate vector of size 1024.0 Mb
R diffbind
8.1 years ago ekgush • 0
0
votes
0
replies
1.2k
views
Bsseq error when use Bsmooth th smooth the object
software error R
8.1 years ago wangk4 • 0
1,163 results • Page 14 of 24
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Comment: gene Set with high AUC score but no cells assigned to cell type by eja.hdrer33ge.r.m • 0
Understanding complex data results like those from AUCell can be challenging. For easier analysis and better data management on the go you …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Votes
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
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