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131
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putting my own expression data in deseq2
DESeq2
updated 15 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Dev
• 0
2
votes
2
replies
226
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
16 days ago • updated 15 days ago
Chris
▴ 10
0
votes
0
replies
90
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
16 days ago
Chris
▴ 10
0
votes
4
replies
260
views
Minfi - estimatecellscount
min
minfi
updated 16 days ago by
James W. MacDonald
65k • written 6 weeks ago by
clacarion
• 0
3
votes
3
replies
259
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 16 days ago by
ATpoint
★ 4.1k • written 16 days ago by
bioinf
▴ 10
0
votes
0
replies
98
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
21 days ago • updated 16 days ago
Sara
• 0
1
vote
1
reply
148
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 18 days ago by
Leo Lahti
▴ 40 • written 19 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
346
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
20 days ago • updated 19 days ago
pl23
• 0
0
votes
2
replies
224
views
PCA plot suggestions
DESeq2
PCAtools
updated 19 days ago by
Michael Love
42k • written 20 days ago by
Aaliya
• 0
1
vote
2
replies
732
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
28 days ago • updated 19 days ago
Patadù
▴ 10
1
vote
3
replies
248
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 19 days ago by
Michael Love
42k • written 19 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
164
views
ATACseq merge peaks
DiffBind
updated 19 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Shloka
• 0
1
vote
4
replies
352
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
21 days ago • updated 19 days ago
winwater0928
• 0
2
votes
9
replies
420
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 19 days ago by
James W. MacDonald
65k • written 20 days ago by
Alexandre
• 0
2
votes
5
replies
255
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
bandconductor
• 0
1
vote
2
replies
172
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
21 days ago • updated 20 days ago
ATpoint
★ 4.1k
0
votes
2
replies
263
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
22 days ago • updated 20 days ago
shuwangxinze1996
• 0
0
votes
8
replies
376
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 20 days ago by
swbarnes2
★ 1.4k • written 22 days ago by
Aaliya
• 0
0
votes
1
reply
164
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 20 days ago by
Michael Love
42k • written 21 days ago by
kcarey
• 0
2
votes
13
replies
467
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
24 days ago • updated 20 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
298
views
get BM error
ensembldb
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
Fara
• 0
0
votes
5
replies
320
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 21 days ago by
James W. MacDonald
65k • written 24 days ago by
Gayatri
• 0
0
votes
0
replies
96
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
21 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
231
views
Different Shrunk Log2FC according with reference
DESeq2
updated 21 days ago by
Michael Love
42k • written 21 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
881
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 21 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
219
views
minfi::read.metharray.exp
minfiData
minfi
updated 21 days ago by
Basti
▴ 780 • written 23 days ago by
clacarion
• 0
3
votes
1
reply
325
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 21 days ago by
Michael Love
42k • written 22 days ago by
i.sudbery
▴ 40
0
votes
7
replies
738
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
10 weeks ago • updated 22 days ago
shepherl
3.9k
1
vote
1
reply
128
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
79
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
22 days ago
info
▴ 10
3
votes
3
replies
245
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 22 days ago by
Michael Love
42k • written 23 days ago by
WardDeb
• 0
0
votes
7
replies
347
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
28 days ago • updated 22 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 22 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 22 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
2
votes
4
replies
270
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 23 days ago by
James W. MacDonald
65k • written 27 days ago by
Mirella Aurora
• 0
4
votes
6
replies
457
views
FilterByExpr low counts with small sample size
edgeR
28 days ago • updated 23 days ago
Jonathan
▴ 10
0
votes
1
reply
133
views
FDR via q-value
qvalue
updated 23 days ago by
James W. MacDonald
65k • written 26 days ago by
John
• 0
6
votes
12
replies
5.0k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 23 days ago
shepherl
3.9k
3
votes
2
replies
226
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 23 days ago by
Guido Hooiveld
★ 4.0k • written 25 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
234
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
26 days ago • updated 23 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 23 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
92
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
24 days ago
vaxahey107
• 0
3
votes
3
replies
362
views
permutation test in edgeR
rna-seq
edgeR
updated 24 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
103
views
I am trying to detect alternative splicing.
ASpli
25 days ago
Sebashish
• 0
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
0
votes
2
replies
811
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
4
replies
257
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
28 days ago • updated 25 days ago
lonn
• 0
1
vote
2
replies
257
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 26 days ago
Weiqian
▴ 10
1
vote
0
replies
328
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
26 days ago
BioinfGuru
▴ 30
1,000 results • Page
3 of 20
Recent ...
Replies
Comment: Create protein sequences including variants from a VCF file
by
Yun
• 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization?
by
Daniel
• 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Guido Hooiveld
★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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