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Views
Votes
2
votes
2
replies
223
views
fgsea significant result
fgsea
13 days ago • updated 12 days ago
Chris
▴ 10
1
vote
2
replies
396
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
Kim
• 0
2
votes
3
replies
261
views
package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by
Gordon Smyth
50k • written 14 days ago by
Patrycja
▴ 20
2
votes
3
replies
253
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Reza
• 0
1
vote
1
reply
184
views
Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by
Michael Love
42k • written 14 days ago by
Zainab
▴ 10
0
votes
0
replies
117
views
dba.plotProfile() plotting and interpretation
DiffBind
14 days ago
Henry
▴ 10
0
votes
6
replies
286
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 13 days ago by
swbarnes2
★ 1.4k • written 15 days ago by
arfranco
▴ 130
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
15 days ago • updated 11 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
z_bahari
• 0
0
votes
1
reply
154
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
c53aba27
• 0
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
15 days ago
tholmes
• 0
0
votes
2
replies
159
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 0
0
votes
0
replies
89
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
15 days ago
yvonneh
• 0
0
votes
0
replies
83
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
15 days ago
Ian D.
▴ 70
0
votes
1
reply
129
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 15 days ago by
4r-rtg
• 0
0
votes
2
replies
207
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 15 days ago
kcarey
• 0
0
votes
3
replies
219
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
james.zhang20
• 0
1
vote
3
replies
302
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 days ago by
ATpoint
★ 4.1k • written 16 days ago by
angelathuynh5
• 0
4
votes
0
replies
134
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
16 days ago
shepherl
3.9k
0
votes
0
replies
135
views
Empty table plot using plotGseaTable()
fgsea
16 days ago • updated 14 days ago
Chris
▴ 10
3
votes
4
replies
268
views
Store output of matchPWM()
biostrings
Biostrings
16 days ago • updated 4 days ago
mat149
▴ 70
0
votes
4
replies
366
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 6 days ago by
Ziliang
• 0 • written 16 days ago by
Ian D.
▴ 70
1
vote
2
replies
287
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
16 days ago • updated 15 days ago
Yveto
• 0
0
votes
3
replies
300
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 days ago by
Michael Love
42k • written 17 days ago by
HAK
• 0
3
votes
4
replies
260
views
Help with error using camera() in limma
CAMERA
limma
17 days ago
Chris
▴ 10
1
vote
1
reply
155
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
marcusn
• 0
0
votes
0
replies
93
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
17 days ago
Maria Doyle
▴ 70
0
votes
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Dev
• 0
0
votes
2
replies
166
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
17 days ago • updated 14 days ago
Aurora
• 0
0
votes
1
reply
122
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 17 days ago by
shepherl
3.9k • written 17 days ago by
bounlu
• 0
0
votes
1
reply
261
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
SSSJec
• 0
0
votes
1
reply
138
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 17 days ago by
Michael Love
42k • written 18 days ago by
Agung
• 0
2
votes
2
replies
233
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 days ago
Chris
▴ 10
0
votes
0
replies
94
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
18 days ago
Chris
▴ 10
0
votes
3
replies
273
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
SSSJec
• 0
3
votes
3
replies
267
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
bioinf
▴ 10
1
vote
1
reply
152
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 21 days ago by
Leo Lahti
▴ 40 • written 21 days ago by
Dario Strbenac
★ 1.5k
1
vote
3
replies
252
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 21 days ago by
Michael Love
42k • written 22 days ago by
JalapenoCornbread
• 0
1
vote
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
22 days ago • updated 21 days ago
pl23
• 0
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
Alexandre
• 0
0
votes
0
replies
142
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
22 days ago • updated 14 days ago
glaciya2018
• 0
0
votes
2
replies
226
views
PCA plot suggestions
DESeq2
PCAtools
updated 21 days ago by
Michael Love
42k • written 22 days ago by
Aaliya
• 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 23 days ago by
Michael Love
42k • written 23 days ago by
kcarey
• 0
0
votes
1
reply
170
views
ATACseq merge peaks
DiffBind
updated 21 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Shloka
• 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
23 days ago • updated 18 days ago
Sara
• 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
23 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
175
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
23 days ago • updated 22 days ago
ATpoint
★ 4.1k
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
355
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
23 days ago • updated 21 days ago
winwater0928
• 0
2
votes
5
replies
303
views
get BM error
ensembldb
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Fara
• 0
45,667 results • Page
2 of 914
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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