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Votes
0
votes
0
replies
168
views
Empty boxes in treemap plot rrvgo package
rrvgo
3 months ago
Asma
• 0
0
votes
3
replies
530
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
3 months ago • updated 12 weeks ago
Shajahan
• 0
3
votes
13
replies
2.0k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
updated 6 hours ago by
shy.hippopotamus.yxmb
• 0 • written 13 months ago by
bioshot.com
• 0
3
votes
2
replies
846
views
Transcript expression analysis using EdgeR
edgeR
Transcript
RNASeq
3 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
206
views
Results with PON give more variants
mutect2
variants
pon
written 3 months ago by
ramiro.barrantes
▴ 10
0
votes
1
reply
248
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
luna.picello
• 0
0
votes
1
reply
575
views
MEDIPS.meth gives table with NA rpkm values
MEDIPS
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
huangdcc
• 0
0
votes
1
reply
916
views
Using offset in edgeR
edgeR
updated 3 months ago by
Gordon Smyth
53k • written 3 months ago by
mmadrzyk
• 0
2
votes
2
replies
1.9k
views
ExperimentHub full metadata
ExperimentHub
written 4 months ago by
igor
▴ 50
1
vote
2
replies
2.5k
views
Non-monotonic voomByGroup plot in Xenium data
XeniumIO
voom
3 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
0
replies
212
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 11 weeks ago by
Michael Love
43k • written 3 months ago by
Sabina
• 0
0
votes
1
reply
613
views
cytolib uses outdated boost call
cytolib
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
machne
• 0
4
votes
8
replies
1.8k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2
edgeR
limma
xenium
Voom
3 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
2
replies
312
views
can't post
devel
updated 3 months ago by
shepherl
4.2k • written 3 months ago by
machne
• 0
7
votes
9
replies
5.6k
views
competitive enrichment test yields too few significant results, self-contained too many
limma
DESeq2
fry
edgeR
3 months ago
bbao
▴ 10
0
votes
1
reply
1.4k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray
limma
BRAIN
Microarray
limma
BRAIN
updated 3 months ago by
Gordon Smyth
53k • written 16.7 years ago by
Dmitriy Verkhoturov
▴ 10
0
votes
2
replies
935
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
Asma
• 0
0
votes
1
reply
495
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport
DESeq2
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
IUH
• 0
3
votes
9
replies
4.5k
views
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 5 days ago by
dan.gatti
• 0 • written 3 months ago by
Fabian
▴ 10
0
votes
0
replies
215
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
3 months ago
Valeria
• 0
0
votes
0
replies
196
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
3 months ago
Wei Shi
★ 3.6k
1
vote
3
replies
2.3k
views
Regarding the issue of background genes in enrichment analysis
KEGG
goTools
seqTools
written 4 months ago by
17506483572
▴ 10
0
votes
3
replies
2.3k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma
Bioconductor
Metabolomics
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
anni
• 0
2
votes
4
replies
3.2k
views
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
diffGeneAnalysis
lncRNA
4 months ago
John
▴ 10
0
votes
2
replies
952
views
gene detection across experiments
DESeq2
Normalization
4 months ago
Mara
• 0
0
votes
3
replies
1.6k
views
RNA-seq: TPM batch effect correction
rnaseqDTU
Normalization
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Samuel
• 0
1
vote
3
replies
1.7k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
written 6 months ago by
Franz Bachmann
• 0
5
votes
11
replies
3.2k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
written 6 months ago by
caroline.zanchi
▴ 10
0
votes
5
replies
1.9k
views
compute_fasta_digest does not match Salmon index hash
tximeta
written 7 months ago by
Alex
• 0
0
votes
5
replies
807
views
WGCNA
WGCNA
Normalization
RNASeq
written 8 months ago by
Vishnu
• 0
3
votes
4
replies
5.1k
views
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler
enrichGO
ComplexHeatmap
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
caroline.zanchi
▴ 10
0
votes
3
replies
1.1k
views
TopGO question
topGO
top
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Hannah
• 0
0
votes
2
replies
1.0k
views
Starting with a clean bioconductor rstudio container
Bioconductor
updated 4 months ago by
ATpoint
★ 5.0k • written 4 months ago by
Ramiro
• 0
0
votes
1
reply
2.4k
views
ChAMP pipeline error (champ.import)
software error
updated 4 months ago by
macdonaldfrench7286566
• 0 • written 6.6 years ago by
mhebba
• 0
0
votes
2
replies
526
views
Problem in Chip-seq data analysis using MACS3
chipseq
MACSdata
updated 4 months ago by
ATpoint
★ 5.0k • written 4 months ago by
Gaurav
• 0
1
vote
5
replies
4.1k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 3 months ago by
Michael Love
43k • written 4 months ago by
Alexander
• 0
0
votes
1
reply
690
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Nicholas
• 0
1
vote
1
reply
2.1k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2
multifactorialdesign
interaction
InteractionSet
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Integrative
• 0
0
votes
2
replies
1.1k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Rocio
• 0
0
votes
3
replies
946
views
Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto
tximport
ensembl
updated 4 months ago by
Abbott
• 0 • written 4 months ago by
Nicholas
• 0
1
vote
2
replies
3.7k
views
Is voomByGroup available in limma?
limmaGUI
voom
4 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
4
replies
1.7k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db
zebrafish
limma
4 months ago
Eric
• 0
1
vote
3
replies
1.4k
views
News:
Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt
ensembldb
written 6 months ago by
Aleena_Ensembl
▴ 30
0
votes
0
replies
25
views
Spam:
wealthdt5
weaver
wealth
4 months ago
Enfurry
0
0
votes
0
replies
253
views
Y-axis break ihn Volcano Plot
EnhancedVolcano
Y-axis_break
Volcano_Plot
4 months ago
rajdeepboral00
• 0
0
votes
0
replies
229
views
getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC
hcg110.db
updated 4 months ago by
shepherl
4.2k • written 4 months ago by
zwang072005
• 0
3
votes
2
replies
1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 5 months ago by
Christian
▴ 20
1
vote
2
replies
2.6k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 5 months ago by
corranna98
• 0
0
votes
0
replies
262
views
Job:
Job: Ensembl Dataflow Coordinator
JobPosting
ensembldb
4 months ago
Aleena_Ensembl
▴ 30
0
votes
1
reply
1.3k
views
Retrieve Salmon transcript quantification file from recount3
recount3
updated 4 months ago by
Leonardo Collado Torres
★ 1.1k • written 5 months ago by
kyn
▴ 10
46,658 results • Page
3 of 934
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Comment: Highly DE genes but small count difference within conditions
by
shy.hippopotamus.yxmb
• 0
Monkey Mart: The Ultimate Gaming Marketplace Experience https://monkeymart.one/
Comment: Highly DE genes but small count difference within conditions
by
shy.hippopotamus.yxmb
• 0
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shy.hippopotamus.yxmb
• 0
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Comment: copy number/LOH for Affy 100K
by
igkryycpinmshzugby
• 0
Hi John For copy number and LOH analysis from Affymetrix 100K SNP arrays you can use aroma.affymetrix or CRLMM packages in Bioconductor. …
Comment: Integration: Paired-end vs healthy single-end from a different source
by
igkryycpinmshzugby
• 0
Yes, Option 1 (technical homogenization) reprocessing paired-end samples as single-end using only R1 is the most defensible approach when l…
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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