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84
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News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
12 days ago
Maria Doyle
▴ 70
0
votes
1
reply
125
views
putting my own expression data in deseq2
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Dev
• 0
0
votes
2
replies
148
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
13 days ago • updated 9 days ago
Aurora
• 0
0
votes
1
reply
111
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 12 days ago by
shepherl
3.9k • written 13 days ago by
bounlu
• 0
0
votes
1
reply
250
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 12 days ago by
James W. MacDonald
65k • written 13 days ago by
SSSJec
• 0
0
votes
1
reply
123
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 12 days ago by
Michael Love
42k • written 13 days ago by
Agung
• 0
2
votes
2
replies
216
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
13 days ago
Chris
• 0
0
votes
0
replies
84
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
13 days ago
Chris
• 0
0
votes
3
replies
260
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 12 days ago by
James W. MacDonald
65k • written 13 days ago by
SSSJec
• 0
3
votes
3
replies
254
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 13 days ago by
ATpoint
★ 4.1k • written 14 days ago by
bioinf
▴ 10
1
vote
1
reply
141
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 16 days ago by
Leo Lahti
▴ 40 • written 16 days ago by
Dario Strbenac
★ 1.5k
1
vote
3
replies
238
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 16 days ago by
Michael Love
42k • written 17 days ago by
JalapenoCornbread
• 0
1
vote
7
replies
342
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
17 days ago • updated 16 days ago
pl23
• 0
2
votes
9
replies
407
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
Alexandre
• 0
0
votes
0
replies
132
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
18 days ago • updated 9 days ago
glaciya2018
• 0
0
votes
2
replies
219
views
PCA plot suggestions
DESeq2
PCAtools
updated 16 days ago by
Michael Love
42k • written 18 days ago by
Aaliya
• 0
0
votes
1
reply
161
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 18 days ago by
Michael Love
42k • written 18 days ago by
kcarey
• 0
0
votes
1
reply
154
views
ATACseq merge peaks
DiffBind
updated 16 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Shloka
• 0
0
votes
0
replies
94
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
18 days ago • updated 14 days ago
Sara
• 0
0
votes
0
replies
92
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
18 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
167
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
18 days ago
ATpoint
★ 4.1k
1
vote
3
replies
226
views
Different Shrunk Log2FC according with reference
DESeq2
updated 18 days ago by
Michael Love
42k • written 19 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
345
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 days ago
winwater0928
• 0
2
votes
5
replies
288
views
get BM error
ensembldb
updated 18 days ago by
James W. MacDonald
65k • written 19 days ago by
Fara
• 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 17 days ago by
James W. MacDonald
65k • written 19 days ago by
bandconductor
• 0
1
vote
1
reply
184
views
Citation for edgeR user guide
edgeR
updated 19 days ago by
Gordon Smyth
50k • written 19 days ago by
k___
▴ 30
3
votes
1
reply
319
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
i.sudbery
▴ 40
1
vote
1
reply
123
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
363
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 18 days ago by
swbarnes2
★ 1.4k • written 19 days ago by
Aaliya
• 0
0
votes
0
replies
77
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
19 days ago
info
▴ 10
0
votes
2
replies
259
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
20 days ago • updated 18 days ago
shuwangxinze1996
• 0
0
votes
2
replies
177
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 20 days ago by
taur.vil
• 0
3
votes
3
replies
235
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 19 days ago by
Michael Love
42k • written 20 days ago by
WardDeb
• 0
1
vote
4
replies
216
views
minfi::read.metharray.exp
minfiData
minfi
updated 19 days ago by
Basti
▴ 780 • written 20 days ago by
clacarion
• 0
1
vote
2
replies
198
views
Improving the design matrices vignette in RNAseq123
RNAseq123
20 days ago • updated 6 days ago
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
310
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 18 days ago by
James W. MacDonald
65k • written 21 days ago by
Gayatri
• 0
2
votes
13
replies
453
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
21 days ago • updated 18 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
86
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
22 days ago
vaxahey107
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
22 days ago • updated 11 days ago
Chris
• 0
0
votes
0
replies
102
views
I am trying to detect alternative splicing.
ASpli
22 days ago
Sebashish
• 0
3
votes
2
replies
220
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 20 days ago by
Guido Hooiveld
★ 3.9k • written 23 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
131
views
FDR via q-value
qvalue
updated 20 days ago by
James W. MacDonald
65k • written 23 days ago by
John
• 0
0
votes
2
replies
224
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
23 days ago • updated 20 days ago
catv
• 0
0
votes
3
replies
165
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
bas_work
▴ 30
1
vote
0
replies
315
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
23 days ago
BioinfGuru
▴ 30
0
votes
2
replies
142
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
24 days ago • updated 23 days ago
prity6459
• 0
2
votes
2
replies
200
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 23 days ago by
James W. MacDonald
65k • written 24 days ago by
sansan
• 0
0
votes
4
replies
211
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
24 days ago
sropri
• 0
1
vote
4
replies
256
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 20 days ago by
James W. MacDonald
65k • written 24 days ago by
Mirella Aurora
• 0
0
votes
3
replies
197
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 23 days ago by
Gordon Smyth
50k • written 24 days ago by
prity6459
• 0
189 results • Page
2 of 4
Recent ...
Replies
Comment: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
zzrammal
• 0
thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ziliang
• 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont
by
Denis
• 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: minfi latest update for EPIC V2 chip
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
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