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0
replies
15
views
Dominance Index for Shotgun Metagenomics Data
microbiome
11 hours ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
90
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 9 hours ago by
Michael Love
41k • written 1 day ago by
JalapenoCornbread
• 0
1
vote
7
replies
135
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
1 day ago • updated 5 hours ago
pl23
• 0
2
votes
9
replies
272
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
Alexandre
• 0
0
votes
0
replies
35
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
1 day ago
glaciya2018
• 0
0
votes
2
replies
99
views
PCA plot suggestions
DESeq2
PCAtools
updated 7 hours ago by
Michael Love
41k • written 1 day ago by
Aaliya
• 0
0
votes
1
reply
81
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 2 days ago by
Michael Love
41k • written 2 days ago by
kcarey
• 0
0
votes
1
reply
51
views
ATACseq merge peaks
DiffBind
updated 10 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
Shloka
• 0
0
votes
0
replies
24
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
2 days ago
Sara
• 0
0
votes
0
replies
33
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
2 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
93
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
2 days ago • updated 1 day ago
ATpoint
★ 4.0k
1
vote
3
replies
120
views
Different Shrunk Log2FC according with reference
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
188
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 16 hours ago
winwater0928
• 0
2
votes
5
replies
158
views
get BM error
ensembldb
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
Fara
• 0
2
votes
5
replies
153
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 1 day ago by
James W. MacDonald
65k • written 3 days ago by
bandconductor
• 0
1
vote
1
reply
92
views
Citation for edgeR user guide
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
k___
▴ 30
3
votes
1
reply
227
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
i.sudbery
▴ 40
1
vote
1
reply
64
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
244
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 1 day ago by
swbarnes2
★ 1.3k • written 3 days ago by
Aaliya
• 0
0
votes
0
replies
29
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
3 days ago
info
▴ 10
0
votes
2
replies
135
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
3 days ago • updated 1 day ago
shuwangxinze1996
• 0
0
votes
1
reply
98
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
taur.vil
• 0
3
votes
3
replies
174
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
WardDeb
• 0
1
vote
4
replies
144
views
minfi::read.metharray.exp
minfiData
minfi
updated 2 days ago by
Basti
▴ 780 • written 4 days ago by
clacarion
• 0
0
votes
1
reply
91
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 14 hours ago by
Gordon Smyth
50k • written 4 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
233
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
Gayatri
• 0
1
vote
13
replies
283
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
5 days ago • updated 2 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
44
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
5 days ago
vaxahey107
• 0
12
votes
12
replies
790
views
Why p value inconsistent when using different number of pathway score?
limma
updated 5 days ago by
Robert Castelo
★ 3.3k • written 6 days ago by
Chris
• 0
0
votes
0
replies
63
views
I am trying to detect alternative splicing.
ASpli
6 days ago
Sebashish
• 0
3
votes
2
replies
165
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 7 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
87
views
FDR via q-value
qvalue
updated 4 days ago by
James W. MacDonald
65k • written 7 days ago by
John
• 0
0
votes
2
replies
160
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
7 days ago • updated 4 days ago
catv
• 0
0
votes
3
replies
105
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
bas_work
▴ 30
1
vote
0
replies
208
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
7 days ago
BioinfGuru
▴ 30
0
votes
2
replies
92
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
7 days ago
prity6459
• 0
2
votes
2
replies
144
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 7 days ago by
James W. MacDonald
65k • written 8 days ago by
sansan
• 0
0
votes
4
replies
138
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
8 days ago
sropri
• 0
1
vote
4
replies
159
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 4 days ago by
James W. MacDonald
65k • written 8 days ago by
Mirella Aurora
• 0
0
votes
3
replies
133
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
prity6459
• 0
0
votes
0
replies
88
views
Warning while loading DEP package
DEP
updated 8 days ago by
shepherl
3.8k • written 8 days ago by
Namrata
• 0
0
votes
1
reply
87
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 8 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Alessia
• 0
0
votes
1
reply
94
views
rlog transformation
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
ishij9717
• 0
0
votes
1
reply
90
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 8 days ago by
Michael Love
41k • written 8 days ago by
09191919
• 0
3
votes
1
reply
122
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
184
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
8 days ago
Le
• 0
1
vote
2
replies
128
views
Error in champ.load(): The following specified files do not exist
ChAMP
9 days ago • updated 8 days ago
Sherin
• 0
0
votes
1
reply
81
views
Input Question for deseq.r
RSeqAn
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
Nina
• 0
4
votes
6
replies
347
views
FilterByExpr low counts with small sample size
edgeR
9 days ago • updated 4 days ago
Jonathan
▴ 10
0
votes
4
replies
200
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
9 days ago • updated 6 days ago
lonn
• 0
1,000 results • Page
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Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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