Showing : r • reset
1
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2
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182
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
26 days ago • updated 12 days ago jbnrodriguez • 0
2
votes
2
replies
88
views
DiffBind (Error in if (DBA$config$parallelPackage))
parallel R DiffBind
4 weeks ago eggrandio • 0
0
votes
1
reply
127
views
hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R pheatmap xcms
updated 5 weeks ago by 3.4k • written 5 weeks ago by • 0
0
votes
0
replies
59
views
How to assign custom colour codes for Multiple sequence alignment (MSA)?
Phylogenetics genomes R MultipleSequenceAlignment Bioconductor
6 weeks ago • updated 5 weeks ago K. • 0
0
votes
0
replies
68
views
EnrichGO
R enrichplot
updated 6 weeks ago by 3.4k • written 6 weeks ago by • 0
0
votes
1
reply
121
views
python and R
snpeff python tophat r RNAseq123
updated 8 weeks ago by 3.4k • written 8 weeks ago by • 0
2
votes
6
replies
257
views
How can I use geom_label_repel with EnhancedVolcano?
ggrepel RNASeq R EnhancedVolcano
9 weeks ago Loren ▴ 10
1
vote
3
replies
168
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 9 weeks ago by ▴ 70 • written 9 weeks ago by • 0
0
votes
2
replies
141
views
Help with Limma design matrix
limma R
10 weeks ago • updated 7 weeks ago lintek08 • 0
1
vote
7
replies
191
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
11 weeks ago • updated 10 weeks ago pegah.taklifi ▴ 30
0
votes
1
reply
150
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 10 weeks ago by ▴ 70 • written 11 weeks ago by • 0
2
votes
3
replies
252
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 10 weeks ago by 34k • written 3 months ago by • 0
1
vote
3
replies
168
views
How to write a script for identifying associate gene id
bash r bingo
3 months ago • updated 9 weeks ago abhisekdey061 • 0
0
votes
0
replies
177
views
R: STRINGdb, from get_enrichment() function how to get background gene list that are related to pathways?
R STRINGdb
3 months ago choijamts • 0
0
votes
1
reply
183
views
Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 4 months ago by 34k • written 4 months ago by • 0
1
vote
4
replies
326
views
Need help in running GO analysis
RNASeq R
4 months ago Rishav ▴ 20
0
votes
0
replies
107
views
Need help in understanding MSstatsTMT package
R
4 months ago Rishav ▴ 20
1
vote
1
reply
160
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 4 months ago by ▴ 700 • written 4 months ago by • 0
0
votes
3
replies
254
views
Error installing Deseq2
DESeq2 R
4 months ago GA ▴ 10
0
votes
1
reply
373
views
"No genes can be mapped...." using enrichGO in clusterProfiler
R TAIR clusterProfiler enrichGO Arabidopsis
updated 4 months ago by ★ 3.0k • written 4 months ago by • 0
2
votes
3
replies
212
views
Compute fgsea with my own database with R version 4.0.2
R fgsea
updated 4 months ago by ▴ 200 • written 4 months ago by • 0
4
votes
8
replies
551
views
Is there a different way to generate a tree for phyloseq object
r dada2 Bioconductor
updated 4 months ago by ▴ 980 • written 4 months ago by ▴ 10
2
votes
2
replies
173
views
How to overcome issue linked to loading big R object
minfi R methylation
4 months ago Federica ▴ 10
4
votes
2
replies
350
views
Error Loading "org.Dm.eg.db" package
r org.Dm.eg.db
updated 5 months ago by ▴ 80 • written 5 months ago by ▴ 20
0
votes
2
replies
213
views
I want to use global test.
gene r clst rpy globaltest
5 months ago Kim • 0
1
vote
7
replies
414
views
Error with hclust
dendrogram hclust textanalysis R RStudio
5 months ago Abby ▴ 10
0
votes
4
replies
708
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 6 months ago by ▴ 270 • written 6 months ago by ▴ 10
0
votes
0
replies
192
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq pathview statistics R
6 months ago • updated 4 months ago Luo Weijun ★ 1.5k
0
votes
0
replies
174
views
Limma design multi-level experiment with 3 time points
R proteomics limma
6 months ago ellen2270 • 0
1
vote
4
replies
294
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
6 months ago tpm • 0
0
votes
1
reply
363
views
Can you colour dendrogram branch clusters in pheatmap?
R heatmaps pheatmap
updated 6 months ago by 3.4k • written 6 months ago by ▴ 10
0
votes
2
replies
240
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
updated 7 months ago by 25k • written 7 months ago by • 0
0
votes
1
reply
345
views
plotSex error message
minfiData plotsex minfi minfiDataEPIC r
updated 7 months ago by • 0 • written 7 months ago by • 0
0
votes
1
reply
196
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 7 months ago by ▴ 150 • written 7 months ago by • 0
1
vote
2
replies
207
views
Incomplete GWAS Catalog Data from makeCurrentGwascat()
gwascat r
8 months ago anailis • 0
2
votes
4
replies
563
views
R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error mac DESeq2 GenomeInfoDb R
8 months ago • updated 7 months ago Dan ▴ 10
0
votes
2
replies
254
views
Add ticks to scale_x_flowjo_biexp()?
R CytoML ggycto
updated 9 months ago by ★ 1.3k • written 9 months ago by • 0
1
vote
3
replies
253
views
Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression R limma MultipleComparison
updated 9 months ago by 58k • written 9 months ago by • 0
0
votes
2
replies
765
views
Add selected row names on pheatmap
R pheatmap
updated 9 months ago by ▴ 850 • written 9 months ago by • 0
5
votes
6
replies
421
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
10 months ago ecg1g15 • 0
7
votes
5
replies
477
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
10 months ago ecg1g15 • 0
0
votes
0
replies
220
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R statistics pathview singlecellRNA-Seq
10 months ago • updated 6 months ago Luo Weijun ★ 1.5k
0
votes
1
reply
211
views
I am using the DEP package example dataset, and I am getting this error on: plot_frequency(data_se)
DEP R Bioconductor Plot
updated 10 months ago by 2.8k • written 10 months ago by • 0
0
votes
3
replies
515
views
Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode : logical
R DESeq2
10 months ago Ricard Lambea • 0
2
votes
6
replies
828
views
Cannot download “EBImage” library in R
R EBImage
written 10 months ago by • 0
0
votes
0
replies
258
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
11 months ago mmartin ▴ 20
0
votes
1
reply
267
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 11 months ago by 58k • written 11 months ago by • 0
2
votes
4
replies
306
views
Bioconductor package development
package R software development
updated 12 months ago by 25k • written 12 months ago by • 0
0
votes
1
reply
224
views
Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 9 months ago by • 0 • written 14 months ago by • 0
1
vote
3
replies
528
views
Convert mouse gene ids to hamster gene ids
biomart R ensembl
updated 5 months ago by 3.4k • written 14 months ago by • 0
50 results • Page 1 of 1
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Comment: rtracklayer: error in importing bigwig file in r in windows by Leonardo Collado Torres ▴ 930
Hi, `rtracklayer::import.bw()` is supposed to work on Windows nowadays, but well, I see that I still avoid it on several pieces of `derfin…
Answer: Microarray - Illumina Metadata by James W. MacDonald 58k
It's not exactly clear to me what you are after, but I'll take a stab at it. First off you probably want to read in using the `GEOquery` pa…
Answer: Can VST be run without runing DESeq or estimateSizeFactors by ATpoint ▴ 850
Just run it, the necessary steps are taken care of internally. You do not have to do anything other than `vst()`.
Comment: GenomicScores package: availableGScores and getGScores functions not working by Robert Castelo ★ 2.7k
Hi, just in case for future users with a similar problem. The package doesn't seem to work with the resources downloaded from the Annotatio…
Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0
EDIT: Ignore this, re-read the warning message in more detail (belatedly). I am now moving the cache. Thanks for the reply, I have since u…
Votes
A: Extracting normalized counts in MEDIPS
Creating qPCRset for nondetects anlaysis from QuantStudio data
Comment: Extracting normalized counts in MEDIPS
Creating qPCRset for nondetects anlaysis from QuantStudio data
Answer: DESeq2 fold change filtering
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