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1.6k
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2
independentfiltering
glmGamPoi
17 months ago • updated 16 months ago
Bob
▴ 30
0
votes
1
reply
644
views
Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2
NanoporeRNASeq
DNASeq
updated 16 months ago by
Michael Love
43k • written 17 months ago by
Dot
• 0
0
votes
2
replies
1.1k
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 16 months ago by
nrenke
• 0 • written 16 months ago by
Lucie
• 0
3
votes
3
replies
1.0k
views
One-sided tests with CAMERA-PR
CAMERA
limma
updated 16 months ago by
Gordon Smyth
53k • written 17 months ago by
Tyler Sagendorf
▴ 10
0
votes
2
replies
997
views
FlowSOM library requires igraph but igraph does not install
FlowSOM
updated 8 months ago by
Szabolcs
• 0 • written 16 months ago by
Priyanka
• 0
0
votes
2
replies
536
views
get_snp
frmaTools
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
Hans
• 0
0
votes
0
replies
582
views
hichip fragments extraction chip seq
ChIPSeqData
interact
GenomicRanges
HiC
16 months ago
user_bioinfo
• 0
0
votes
3
replies
1.1k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2
edgeR
DifferentialExpression
written 17 months ago by
dancingcow
• 0
3
votes
5
replies
2.4k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2
RNAseq
DifferentialExpression
updated 17 months ago by
swbarnes2
★ 1.4k • written 17 months ago by
BioNovice247
• 0
2
votes
1
reply
1.7k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2
heatmaps
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
jeba95
• 0
0
votes
1
reply
644
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
17 months ago • updated 16 months ago
mdidish
▴ 10
0
votes
0
replies
547
views
DiffBind dba.plotprofile y-axis range
DiffBind
17 months ago
Tara
• 0
2
votes
4
replies
882
views
Bioconductor Submission question
Bioconductor
17 months ago
XFWu
• 0
2
votes
3
replies
1.4k
views
RUV - Does my data need further normalisation?
EDASeq
plotRLE
RNAseq
17 months ago • updated 16 months ago
BioinfGuru
▴ 70
2
votes
2
replies
907
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq
DESeq2
dese
17 months ago
BioinfGuru
▴ 70
0
votes
0
replies
485
views
proActiv-promoter analysis
proActiv
Transcriptomics
17 months ago
wang.xiangyu
• 0
2
votes
1
reply
2.3k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData
Clustering
memory
SingleCellExperiment
edgeR
updated 17 months ago by
Aaron Lun
★ 29k • written 17 months ago by
Joseph
• 0
0
votes
0
replies
579
views
News:
Annual Nominations Open for CAB and TAB! Deadline Aug 31
TAB
CAB
Bioconductor
17 months ago
shepherl
4.2k
1
vote
2
replies
821
views
Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
17 months ago
DL
• 0
0
votes
3
replies
738
views
How to combine multiple lists of cytoframes/cytocq data objects into one
flowWorkspace
cytocq
updated 17 months ago by
SamGG
▴ 360 • written 17 months ago by
anders.tondell
▴ 30
0
votes
1
reply
830
views
edgeR - design a complex matrix
design
model.matrix
edgeR
complexdesign
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Karla
• 0
1
vote
4
replies
1.5k
views
How to Query Only SNPs from the biomaRt Variation Database
biomaRt
17 months ago
kschecht
• 0
0
votes
1
reply
1.2k
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 17 months ago by
Axel Klenk
★ 1.1k • written 17 months ago by
Bioinformagician
• 0
0
votes
0
replies
580
views
EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions - submissions open!
Community
Conference
Bioconductor
EuroBioC2024
17 months ago
Maria Doyle
▴ 110
0
votes
1
reply
718
views
Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData
CEMiTool
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Menna
• 0
3
votes
3
replies
1.1k
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Ahdee
▴ 60
2
votes
3
replies
948
views
EBImage Rendering of a DelayedArray Object
DelayedArray
EBImage
cytomapper
updated 7 months ago by
Hervé Pagès
16k • written 17 months ago by
Dario Strbenac
★ 1.6k
0
votes
3
replies
1.6k
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub
AnnotationDbi
AnnotationForge
17 months ago
Anna
• 0
0
votes
3
replies
937
views
RNA-seq with DESeq2 shrinkage estimation
Regression
DESeq2
rnaseqGene
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
David W. H.
• 0
0
votes
4
replies
1.3k
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts
Subread
Bioconductor
17 months ago
Jessica
• 0
2
votes
8
replies
4.0k
views
biomaRt getLDS error
biomaRt
17 months ago
mark.dunning
▴ 20
1
vote
2
replies
901
views
Question on number of genes used in GO analysis
GO
clusterProfiler
17 months ago
Danté
• 0
6
votes
15
replies
2.6k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 17 months ago by
swbarnes2
★ 1.4k • written 17 months ago by
kubracelikbas4
• 0
0
votes
4
replies
1.0k
views
Failed to install geneLenDataBase
geneLenDataBase
ChAMP
updated 17 months ago by
shepherl
4.2k • written 17 months ago by
Fang
• 0
0
votes
4
replies
1.4k
views
WTChimeraData() Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [experimenthub.bioconductor.org] Connection time-out
WTChimeraData
MouseGastrulationData
WT
17 months ago
haidan
• 0
1
vote
2
replies
1.4k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
17 months ago
grothmn
• 0
4
votes
4
replies
1.8k
views
NAs in fgseaMultilevel
fgsea
updated 17 months ago by
alserg
▴ 280 • written 17 months ago by
Danté
• 0
1
vote
2
replies
970
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts
Rsubread
17 months ago
Anke
• 0
0
votes
8
replies
1.4k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 17 months ago by
Rory Stark
★ 5.2k • written 17 months ago by
Marianna
▴ 20
1
vote
1
reply
1.1k
views
biomaRt getSequence(): Error in .lock2
ensembldb
getSequence
updated 17 months ago by
Mike Smith
★ 6.6k • written 17 months ago by
Melanie
▴ 10
0
votes
2
replies
1.8k
views
save.rnb.set warnings when trying to save rnb.set
RnBeads
RnBeads.hg19
MethylationArray
updated 6 months ago by
juansmurphy
• 0 • written 17 months ago by
hayleyw
• 0
0
votes
5
replies
1.2k
views
preprocessENmix colnames Error
ENmix
Preprocessing
17 months ago
Eve
• 0
0
votes
1
reply
1.3k
views
HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2
LRT
Wald
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Eric
• 0
4
votes
7
replies
2.4k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables
DESeq2
BatchEffect
bulkrna-seq
sva-seq
updated 17 months ago by
jessica.anderson
▴ 10 • written 18 months ago by
BioinfGuru
▴ 70
2
votes
4
replies
1.2k
views
how limma work with continous variables
GordonSmyth
limmaGUI
lmFit
voom
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
adR
▴ 40
0
votes
1
reply
889
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering
DESeq2
outliers
updated 17 months ago by
Michael Love
43k • written 17 months ago by
smac_head
• 0
0
votes
1
reply
1.0k
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2
volcanoplot
LRT
updated 17 months ago by
Michael Love
43k • written 17 months ago by
Eric
• 0
0
votes
1
reply
720
views
Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
seqFISH
SpatialExperiment
17 months ago
Matthew Thornton
▴ 390
5
votes
7
replies
3.4k
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws
AnnotationDbi
written 18 months ago by
georgii.vdovin
• 0
2
votes
3
replies
1.0k
views
Comparing one group against multiple groups in DESeq2
DESeq2
written 23 months ago by
tamivico
• 0
46,705 results • Page
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