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0
votes
5
replies
1.9k
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compute_fasta_digest does not match Salmon index hash
tximeta
written 6 months ago by
Alex
• 0
0
votes
5
replies
703
views
WGCNA
WGCNA
Normalization
RNASeq
written 7 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 12 weeks ago by
James W. MacDonald
68k • written 3 months ago by
caroline.zanchi
▴ 10
0
votes
3
replies
1.1k
views
TopGO question
topGO
top
updated 12 weeks ago by
James W. MacDonald
68k • written 3 months ago by
Hannah
• 0
0
votes
2
replies
958
views
Starting with a clean bioconductor rstudio container
Bioconductor
updated 3 months ago by
ATpoint
★ 4.9k • written 3 months ago by
Ramiro
• 0
0
votes
1
reply
2.3k
views
ChAMP pipeline error (champ.import)
software error
updated 3 months ago by
macdonaldfrench7286566
• 0 • written 6.5 years ago by
mhebba
• 0
0
votes
2
replies
461
views
Problem in Chip-seq data analysis using MACS3
chipseq
MACSdata
updated 3 months ago by
ATpoint
★ 4.9k • written 3 months ago by
Gaurav
• 0
1
vote
5
replies
3.7k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 8 weeks ago by
Michael Love
43k • written 3 months ago by
Alexander
• 0
0
votes
1
reply
638
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 3 months ago by
Michael Love
43k • written 3 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 3 months ago by
Michael Love
43k • written 3 months ago by
Integrative
• 0
0
votes
2
replies
1.1k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Rocio
• 0
0
votes
3
replies
889
views
Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto
tximport
ensembl
updated 12 weeks ago by
Abbott
• 0 • written 3 months ago by
Nicholas
• 0
1
vote
2
replies
3.6k
views
Is voomByGroup available in limma?
limmaGUI
voom
3 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
4
replies
1.6k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db
zebrafish
limma
3 months ago
Eric
• 0
1
vote
3
replies
1.3k
views
News:
Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt
ensembldb
written 4 months ago by
Aleena_Ensembl
▴ 30
0
votes
0
replies
25
views
Spam:
wealthdt5
weaver
wealth
3 months ago
Enfurry
0
0
votes
0
replies
212
views
Y-axis break ihn Volcano Plot
EnhancedVolcano
Y-axis_break
Volcano_Plot
3 months ago
rajdeepboral00
• 0
0
votes
0
replies
184
views
getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC
hcg110.db
updated 3 months ago by
shepherl
4.2k • written 3 months ago by
zwang072005
• 0
3
votes
2
replies
1.3k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 3 months ago by
Christian
▴ 20
1
vote
2
replies
2.5k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 3 months ago by
corranna98
• 0
0
votes
0
replies
220
views
Job:
Job: Ensembl Dataflow Coordinator
JobPosting
ensembldb
3 months ago
Aleena_Ensembl
▴ 30
0
votes
1
reply
1.3k
views
Retrieve Salmon transcript quantification file from recount3
recount3
updated 3 months ago by
Leonardo Collado Torres
★ 1.1k • written 3 months ago by
kyn
▴ 10
0
votes
1
reply
1.1k
views
error from library(IlluminaHumanMethylationMSAmanifest)
MSAarray25
hcg110.db
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
zwang072005
• 0
0
votes
1
reply
854
views
Source / binary version mismatch for rGADEM
rGADEM
updated 3 months ago by
shepherl
4.2k • written 3 months ago by
Jay hesselberth
• 0
0
votes
9
replies
13k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 3 months ago by
Hadi
• 0 • written 4.1 years ago by
charlotte
▴ 10
3
votes
1
reply
3.7k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Chenghao
▴ 10
0
votes
2
replies
1.2k
views
Interaction in Design Experimental
rnaseqGene
3 months ago
Ferdinand David
• 0
0
votes
0
replies
254
views
Job:
Lab Head positions at the WEHI, Melbourne, Australia
JobPosting
Bioconductor
3 months ago
Gordon Smyth
53k
1
vote
4
replies
2.1k
views
Heatmap of the Count Matrix
rnaseqGene
updated 9 days ago by
ArnulfoByrd
• 0 • written 3 months ago by
Ferdinand David
• 0
0
votes
1
reply
442
views
DESeq2 results
result
DESeq2
subsetting
updated 3 months ago by
ATpoint
★ 4.9k • written 3 months ago by
rajdeepboral00
• 0
0
votes
0
replies
169
views
DiffBind plot.profile error
BiocParallel
DiffBind
3 months ago
this_is_me_trying
• 0
0
votes
4
replies
8.4k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
written 2.0 years ago by
Aytaç
• 0
0
votes
4
replies
843
views
Position of the legend object in complexHeatmap
ComplexHeatmap
3 months ago
caroline.zanchi
▴ 10
0
votes
4
replies
3.1k
views
Drawing custom KEGG pathways
pathview
KEGG
written 4.3 years ago by
curiousmind007
▴ 10
1
vote
18
replies
7.2k
views
error in ChAMP loading file
ChAMP
updated 12 weeks ago by
josephasmith1310
• 0 • written 2.8 years ago by
Giulia
• 0
1
vote
4
replies
1.9k
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
5 months ago • updated 6 days ago
Kateřina
• 0
3
votes
2
replies
6.3k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
3 months ago
Geoff
• 0
0
votes
1
reply
817
views
Workflow to Analyse DNA Sequence specify gene expression in a fungus under stress
rnaseqGene
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Ferdinand David
• 0
0
votes
1
reply
361
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Pak
• 0
0
votes
1
reply
421
views
lncRNA functional annotation package
RNAseq123
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
tarek.mohamed
• 0
1
vote
1
reply
610
views
Biomart server error
biomaRt
BioMartGOGeneSets
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
tarek.mohamed
• 0
0
votes
0
replies
9
views
Spam:
Best Piles Clinic in Hyderabad
cadd.v1.6.hg38
BestPilesClinicinHyderabad
hcg110.db
MethylSeekR
3 months ago
Laserqure03
0
0
votes
2
replies
1.7k
views
An ESR essay about software design, and how it applies to Bioconductor
GUI
GUI
written 21.6 years ago by
Ann Loraine
▴ 30
0
votes
1
reply
463
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 3 months ago by
Michael Love
43k • written 4 months ago by
s.malik
• 0
3
votes
2
replies
2.0k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
4 months ago • updated 3 months ago
dudutchy
▴ 10
0
votes
8
replies
1.4k
views
ERCC Spike-In controls being discarded during Tximeta process:
@mikelove
tximeta
updated 3 months ago by
Michael Love
43k • written 4 months ago by
Gaurav
• 0
2
votes
4
replies
2.5k
views
Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics
edgeR
DEG
3 months ago
Maziya
• 0
4
votes
17
replies
5.4k
views
How to load scRNA-seq data from GEO
SingleCellExperiment
GEO
updated 3 months ago by
ATpoint
★ 4.9k • written 4 months ago by
petergrahamclark
▴ 10
2
votes
3
replies
1.2k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
4 months ago • updated 3 months ago
Paulito
• 0
0
votes
1
reply
593
views
Using EBI Image on Ranged Bar Chart
EBImage
written 4 months ago by
ekatcher
• 0
46,633 results • Page
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Comment: DiffBind - question on the use of filtered or unfiltered input data
by
deltaexecutor4
• 0
FFH4X is a [Free Fire mod][1] menu APK that offers cheats like auto headshot, aimbot, ESP, wallhack, and unlimited skins. Players use it to…
Comment: GO.db and others package Download failure
by
James W. MacDonald
68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure
by
James W. MacDonald
68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure
by
Skyler
• 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure
by
James W. MacDonald
68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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