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2
replies
1.3k
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
20 months ago
mohammedtoufiq91
▴ 10
4
votes
3
replies
1.3k
views
recount3 problem downloading data from source sra
recount3
updated 20 months ago by
Leonardo Collado Torres
★ 1.1k • written 20 months ago by
PABLO ANTONIO
▴ 10
0
votes
6
replies
1.7k
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
updated 20 months ago by
kred
• 0 • written 20 months ago by
minardsmitha
▴ 10
1
vote
1
reply
786
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Tim Barry
• 0
0
votes
0
replies
429
views
Conditional analysis
GENESIS
20 months ago
SuperDad
• 0
0
votes
0
replies
1.1k
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
20 months ago
Raghad
• 0
0
votes
2
replies
1.1k
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
20 months ago
landenshanie
▴ 40
2
votes
10
replies
1.7k
views
How to run allelic imbalance in apeglm
apeglm
20 months ago • updated 19 months ago
euge.eugenio
▴ 20
0
votes
1
reply
1.6k
views
ERROR; return code from pthread_create() is 22
affy
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
pickingastar
• 0
1
vote
3
replies
1.1k
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
boczniak767
▴ 740
0
votes
0
replies
684
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
20 months ago
pierre.devillemereuil
• 0
1
vote
2
replies
876
views
Subsetting RNAseq data | voomaByGroup()
limma
20 months ago
Anna
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
20 months ago
shahrozimmac
0
0
votes
0
replies
540
views
Processing of curatedmetagenomics
curatedMetagenomicData
20 months ago
Edward
• 0
7
votes
6
replies
1.8k
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 21 months ago by
robersy
• 0
0
votes
5
replies
1.8k
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
20 months ago
Galina
• 0
0
votes
0
replies
699
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
20 months ago
Bibi
• 0
0
votes
6
replies
1.7k
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
20 months ago
Ken C
• 0
2
votes
4
replies
1.2k
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 20 months ago by
Michael Love
43k • written 20 months ago by
shaunpeterson
• 0
0
votes
0
replies
628
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
20 months ago
Abiologist
• 0
0
votes
3
replies
1.6k
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 20 months ago by
damian.szk
▴ 110 • written 20 months ago by
ninidea
• 0
0
votes
2
replies
852
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
20 months ago
makala
• 0
2
votes
2
replies
1.4k
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
20 months ago
Matthew Thornton
▴ 390
0
votes
0
replies
603
views
determine k during RUVSeq
RUVSeq
RUVnormalize
20 months ago
Ειρήνη
• 0
2
votes
3
replies
1.2k
views
Problem installing ChAMP on a MacBook
ChAMP
updated 20 months ago by
shepherl
4.3k • written 20 months ago by
Galia
• 0
0
votes
1
reply
794
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
updated 17 months ago by
jg
▴ 20 • written 20 months ago by
Shaimaa Gamal
• 0
0
votes
0
replies
16
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
20 months ago
oliverelijhan
0
0
votes
0
replies
591
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
20 months ago
Anton01
• 0
0
votes
0
replies
549
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
20 months ago
danalvoronov
▴ 10
0
votes
0
replies
594
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
20 months ago
k200987
• 0
3
votes
5
replies
1.5k
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
20 months ago
Patadù
▴ 20
0
votes
4
replies
1.6k
views
error running enricher from clusterprofiler
clusterProfiler
cluster
20 months ago
Yael
• 0
3
votes
3
replies
1.3k
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Guillermo
• 0
2
votes
1
reply
862
views
How to design DEXSeq formula for multiple variables
DEXSeq
20 months ago • updated 19 months ago
Sara
• 0
4
votes
9
replies
1.5k
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
pangtaihin
• 0
0
votes
0
replies
568
views
Difference in Contrast in DiffBind
DiffBind
20 months ago
user_bioinfo
• 0
1
vote
2
replies
1.1k
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
20 months ago
Patadù
▴ 20
10
votes
11
replies
3.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 20 months ago by
Sara
• 0 • written 8.4 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
846
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Kasper
• 0
0
votes
2
replies
2.4k
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 20 months ago by
zhouwanding
▴ 20 • written 20 months ago by
Seungmin
• 0
1
vote
0
replies
930
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
22 months ago • updated 20 months ago
shepherl
4.3k
1
vote
2
replies
1.1k
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
20 months ago
Daniel
• 0
0
votes
1
reply
845
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 20 months ago by
Michael Love
43k • written 20 months ago by
piemmea
• 0
1
vote
0
replies
1.2k
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
20 months ago
Aleena_Ensembl
▴ 30
1
vote
2
replies
711
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 20 months ago by
Researcher
▴ 10
0
votes
9
replies
2.5k
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 20 months ago by
BioinfGuru
▴ 70 • written 20 months ago by
Eric Katagirya
• 0
1
vote
3
replies
1.2k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Ashley
• 0
3
votes
4
replies
1.0k
views
Store output of matchPWM()
biostrings
Biostrings
21 months ago • updated 20 months ago
mat149
▴ 80
1
vote
2
replies
1.2k
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
20 months ago
BioinfGuru
▴ 70
0
votes
2
replies
728
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
20 months ago
Yveto
• 0
46,738 results • Page
24 of 935
Recent ...
Replies
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error
by
ansley.r.burtch
• 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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