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0
votes
1
reply
832
views
Problem in execuation of filterAndTrim command in DADA2
Bioconductor
dada2
18 months ago • updated 17 months ago
abhisek001
• 0
3
votes
2
replies
1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
18 months ago
mohammedtoufiq91
▴ 10
4
votes
3
replies
1.2k
views
recount3 problem downloading data from source sra
recount3
updated 18 months ago by
Leonardo Collado Torres
★ 1.1k • written 18 months ago by
PABLO ANTONIO
▴ 10
0
votes
6
replies
1.6k
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
updated 18 months ago by
kred
• 0 • written 18 months ago by
minardsmitha
▴ 10
1
vote
1
reply
698
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Tim Barry
• 0
0
votes
0
replies
409
views
Conditional analysis
GENESIS
18 months ago
SuperDad
• 0
0
votes
0
replies
1.0k
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
18 months ago
Raghad
• 0
0
votes
2
replies
1.1k
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
18 months ago
landenshanie
▴ 40
2
votes
10
replies
1.6k
views
How to run allelic imbalance in apeglm
apeglm
18 months ago
euge.eugenio
▴ 20
0
votes
1
reply
1.5k
views
ERROR; return code from pthread_create() is 22
affy
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
pickingastar
• 0
1
vote
3
replies
1.0k
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
boczniak767
▴ 740
0
votes
0
replies
621
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
18 months ago
pierre.devillemereuil
• 0
1
vote
2
replies
806
views
Subsetting RNAseq data | voomaByGroup()
limma
18 months ago
Anna
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
18 months ago
shahrozimmac
0
0
votes
0
replies
436
views
Processing of curatedmetagenomics
curatedMetagenomicData
18 months ago
Edward
• 0
7
votes
6
replies
1.7k
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 19 months ago by
robersy
• 0
0
votes
5
replies
1.6k
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
18 months ago
Galina
• 0
0
votes
0
replies
650
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
18 months ago
Bibi
• 0
0
votes
6
replies
1.6k
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
18 months ago
Ken C
• 0
2
votes
4
replies
1.1k
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 18 months ago by
Michael Love
43k • written 18 months ago by
shaunpeterson
• 0
0
votes
0
replies
558
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
18 months ago
Abiologist
• 0
0
votes
3
replies
1.4k
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 18 months ago by
damian.szk
▴ 110 • written 18 months ago by
ninidea
• 0
0
votes
2
replies
746
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
18 months ago
makala
• 0
2
votes
2
replies
1.2k
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
19 months ago • updated 18 months ago
Matthew Thornton
▴ 390
0
votes
0
replies
539
views
determine k during RUVSeq
RUVSeq
RUVnormalize
18 months ago
Ειρήνη
• 0
2
votes
3
replies
1.1k
views
Problem installing ChAMP on a MacBook
ChAMP
updated 18 months ago by
shepherl
4.2k • written 18 months ago by
Galia
• 0
0
votes
1
reply
730
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
updated 15 months ago by
jg
▴ 20 • written 18 months ago by
Shaimaa Gamal
• 0
0
votes
0
replies
16
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
18 months ago
oliverelijhan
0
0
votes
0
replies
518
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
18 months ago
Anton01
• 0
0
votes
0
replies
500
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
18 months ago
danalvoronov
▴ 10
0
votes
0
replies
529
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
18 months ago
k200987
• 0
3
votes
5
replies
1.4k
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
18 months ago
Patadù
▴ 20
0
votes
4
replies
1.5k
views
error running enricher from clusterprofiler
clusterProfiler
cluster
18 months ago
Yael
• 0
3
votes
3
replies
1.2k
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Guillermo
• 0
2
votes
1
reply
794
views
How to design DEXSeq formula for multiple variables
DEXSeq
19 months ago • updated 18 months ago
Sara
• 0
4
votes
9
replies
1.4k
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
pangtaihin
• 0
0
votes
0
replies
518
views
Difference in Contrast in DiffBind
DiffBind
18 months ago
user_bioinfo
• 0
1
vote
2
replies
971
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
18 months ago
Patadù
▴ 20
10
votes
11
replies
3.2k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 18 months ago by
Sara
• 0 • written 8.3 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
789
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 18 months ago by
Michael Love
43k • written 19 months ago by
Kasper
• 0
0
votes
2
replies
2.1k
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 19 months ago by
zhouwanding
▴ 20 • written 19 months ago by
Seungmin
• 0
1
vote
0
replies
885
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
20 months ago • updated 19 months ago
shepherl
4.2k
1
vote
2
replies
961
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
19 months ago • updated 18 months ago
Daniel
• 0
0
votes
1
reply
767
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 19 months ago by
Michael Love
43k • written 19 months ago by
piemmea
• 0
1
vote
0
replies
1.0k
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
19 months ago
Aleena_Ensembl
▴ 30
1
vote
2
replies
662
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 19 months ago by
Researcher
▴ 10
0
votes
9
replies
2.3k
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 18 months ago by
BioinfGuru
▴ 70 • written 19 months ago by
Eric Katagirya
• 0
1
vote
3
replies
1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
Ashley
• 0
3
votes
4
replies
956
views
Store output of matchPWM()
biostrings
Biostrings
19 months ago
mat149
▴ 80
1
vote
2
replies
1.1k
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
19 months ago • updated 18 months ago
BioinfGuru
▴ 70
46,691 results • Page
23 of 934
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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68k
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