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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
just now
marcusn
• 0
0
votes
0
replies
1
view
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
just now
Maria Doyle
▴ 70
0
votes
1
reply
18
views
putting my own expression data in deseq2
DESeq2
updated 2 hours ago by
ATpoint
★ 4.1k • written 3 hours ago by
Dev
• 0
0
votes
0
replies
20
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
5 hours ago
Aurora
• 0
0
votes
1
reply
20
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 10 minutes ago by
shepherl
3.8k • written 8 hours ago by
bounlu
• 0
0
votes
0
replies
11
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
9 hours ago
SSSJec
• 0
0
votes
0
replies
23
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
16 hours ago
Agung
• 0
2
votes
2
replies
114
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 hours ago • updated 16 hours ago
Chris
• 0
0
votes
0
replies
31
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
22 hours ago • updated 19 hours ago
Chris
• 0
0
votes
2
replies
113
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
22 hours ago • updated 9 hours ago
SSSJec
• 0
3
votes
3
replies
157
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
bioinf
▴ 10
1
vote
1
reply
93
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 3 days ago by
Leo Lahti
▴ 40 • written 4 days ago by
Dario Strbenac
★ 1.5k
1
vote
3
replies
164
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 3 days ago by
Michael Love
41k • written 4 days ago by
JalapenoCornbread
• 0
1
vote
7
replies
252
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
4 days ago • updated 3 days ago
pl23
• 0
2
votes
9
replies
321
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
Alexandre
• 0
0
votes
0
replies
60
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
5 days ago
glaciya2018
• 0
0
votes
2
replies
154
views
PCA plot suggestions
DESeq2
PCAtools
updated 3 days ago by
Michael Love
41k • written 5 days ago by
Aaliya
• 0
0
votes
1
reply
114
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 5 days ago by
Michael Love
41k • written 5 days ago by
kcarey
• 0
0
votes
1
reply
93
views
ATACseq merge peaks
DiffBind
updated 3 days ago by
ATpoint
★ 4.1k • written 5 days ago by
Shloka
• 0
0
votes
0
replies
58
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
5 days ago • updated 1 day ago
Sara
• 0
0
votes
0
replies
61
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
5 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
123
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
6 days ago • updated 5 days ago
ATpoint
★ 4.1k
1
vote
3
replies
185
views
Different Shrunk Log2FC according with reference
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
272
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
6 days ago • updated 4 days ago
winwater0928
• 0
2
votes
5
replies
223
views
get BM error
ensembldb
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
Fara
• 0
2
votes
5
replies
201
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 4 days ago by
James W. MacDonald
65k • written 6 days ago by
bandconductor
• 0
1
vote
1
reply
145
views
Citation for edgeR user guide
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
k___
▴ 30
3
votes
1
reply
276
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
i.sudbery
▴ 40
1
vote
1
reply
90
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
304
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 5 days ago by
swbarnes2
★ 1.3k • written 6 days ago by
Aaliya
• 0
0
votes
0
replies
49
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
6 days ago
info
▴ 10
0
votes
2
replies
200
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
7 days ago • updated 5 days ago
shuwangxinze1996
• 0
0
votes
1
reply
119
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
taur.vil
• 0
3
votes
3
replies
200
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
WardDeb
• 0
1
vote
4
replies
180
views
minfi::read.metharray.exp
minfiData
minfi
updated 6 days ago by
Basti
▴ 780 • written 7 days ago by
clacarion
• 0
1
vote
1
reply
133
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 4 days ago by
Gordon Smyth
50k • written 8 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
276
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 5 days ago by
James W. MacDonald
65k • written 8 days ago by
Gayatri
• 0
1
vote
13
replies
350
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
8 days ago • updated 5 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
67
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
9 days ago
vaxahey107
• 0
13
votes
16
replies
1.0k
views
Why p value inconsistent when using different number of pathway score?
limma
updated 12 hours ago by
Gordon Smyth
50k • written 9 days ago by
Chris
• 0
0
votes
0
replies
84
views
I am trying to detect alternative splicing.
ASpli
9 days ago
Sebashish
• 0
3
votes
2
replies
190
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 8 days ago by
Guido Hooiveld
★ 3.9k • written 10 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
105
views
FDR via q-value
qvalue
updated 7 days ago by
James W. MacDonald
65k • written 10 days ago by
John
• 0
0
votes
2
replies
181
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
10 days ago • updated 8 days ago
catv
• 0
0
votes
3
replies
124
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
bas_work
▴ 30
1
vote
0
replies
235
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
11 days ago • updated 10 days ago
BioinfGuru
▴ 30
0
votes
2
replies
113
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
11 days ago
prity6459
• 0
2
votes
2
replies
164
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 10 days ago by
James W. MacDonald
65k • written 11 days ago by
sansan
• 0
0
votes
4
replies
166
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
11 days ago
sropri
• 0
1
vote
4
replies
191
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 7 days ago by
James W. MacDonald
65k • written 11 days ago by
Mirella Aurora
• 0
45,592 results • Page
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Answer: Version 3.15 S4Vectors packages are missing
by
shepherl
3.8k
It is missing because that package did not have any updates in the release except for the initial version. The archive directory holds prev…
Comment: putting my own expression data in deseq2
by
ATpoint
★ 4.1k
> directly from GEOquery I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your questi…
Comment: Assist me in determining whether the analysis process using the limma package ha
by
SSSJec
• 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
Chris
• 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
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Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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