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0
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8
views
covariate with negative and positive values
DESeq2
29 minutes ago
Brynn
• 0
0
votes
0
replies
16
views
Adding columns to DEXSeqResults object
DEXSeq
3 hours ago
Clyde
• 0
0
votes
0
replies
17
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
4 hours ago • updated 1 hour ago
Maliha Tabassum
• 0
0
votes
4
replies
82
views
flowStats Search Error
flowStats
updated 4 hours ago by
shepherl
3.8k • written 23 hours ago by
tholmes
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 5 hours ago
shepherl
3.8k
0
votes
1
reply
64
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 6 hours ago by
James W. MacDonald
65k • written 3 days ago by
tian.liu0720
• 0
1
vote
2
replies
43
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
7 hours ago
Ana
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
47
views
what is the sampleFiles
chipseq
updated 8 hours ago by
James W. MacDonald
65k • written 12 hours ago by
zhulin
• 0
0
votes
1
reply
82
views
Differentially expressed genes in monocle pseudotime
monocle
updated 12 hours ago by
Gordon Smyth
50k • written 2 days ago by
kthapa
• 0
3
votes
7
replies
231
views
Memory errors using read.bismark?
dmrseq
bsseq
5 days ago • updated 7 hours ago
Juan Higareda
• 0
0
votes
2
replies
89
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
updated 15 hours ago by
Peter Hickey
▴ 700 • written 4 days ago by
jacques.imbert
• 0
0
votes
1
reply
84
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 16 hours ago by
kamryncole1963
• 0 • written 5 days ago by
Sara
• 0
0
votes
3
replies
108
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 hours ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
0
replies
32
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
1 day ago
Virangika
• 0
0
votes
0
replies
27
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
1 day ago
Henry
▴ 10
1
vote
1
reply
143
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 1 day ago by
Michael Love
41k • written 5 days ago by
Weiqian
▴ 10
0
votes
3
replies
122
views
DEG with low counts
DESeq2
2 days ago • updated 3 hours ago
Rajat
• 0
1
vote
2
replies
173
views
GSVA error
GSVA
2 days ago • updated 1 day ago
Alex
• 0
2
votes
3
replies
194
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
1 day ago • updated 16 hours ago
daniel.carbajo
• 0
3
votes
3
replies
229
views
permutation test in edgeR
rna-seq
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 8 days ago by
Netanel
• 0
1
vote
3
replies
273
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 1 day ago by
Gordon Smyth
50k • written 6 days ago by
Simran
• 0
0
votes
1
reply
71
views
Deseq2 Rlog transformation
DESeq2
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
Sahar
• 0
0
votes
1
reply
648
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 4 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
1
vote
2
replies
123
views
Design Matrix within group comparison more than two groups
DESeq2
4 days ago • updated 3 days ago
hemantcnaik
• 0
0
votes
6
replies
517
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
6 weeks ago • updated 4 days ago
shepherl
3.8k
1
vote
2
replies
119
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
4 days ago
julia_mcdonough
• 0
2
votes
2
replies
107
views
[DiffBind] Obtaining normalization factors
DiffBind
4 days ago • updated 13 hours ago
Henry
▴ 10
0
votes
1
reply
93
views
Bioinformatics student
Des
DESeq2
updated 4 days ago by
hemantcnaik
• 0 • written 4 days ago by
Sahar
• 0
0
votes
0
replies
52
views
Cell type in SVD analysis
ChAMP
4 days ago
simleopold11
• 0
0
votes
0
replies
51
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
4 days ago
shepherl
3.8k
2
votes
2
replies
107
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
4 days ago • updated 1 day ago
daniel.carbajo
• 0
0
votes
2
replies
123
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
4 days ago • updated 9 hours ago
schlumbohm
• 0
3
votes
5
replies
463
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
6 days ago • updated 3 hours ago
Chris
• 0
0
votes
0
replies
55
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
4 days ago
Stevie Pederson
• 0
2
votes
2
replies
320
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 days ago • updated 4 days ago
Henry
▴ 10
0
votes
4
replies
164
views
Storing directories inside an ExperimentHub package?
ExperimentHub
6 days ago • updated 5 days ago
Tim Barry
• 0
0
votes
0
replies
61
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
5 days ago
communication
• 0
3
votes
6
replies
187
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 days ago
nhaus
▴ 30
0
votes
1
reply
124
views
DESeq2 gives an error and R crashes
DESeq2
5 days ago • updated 4 days ago
Shefali
• 0
0
votes
0
replies
87
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
6 days ago
Eryn
• 0
0
votes
0
replies
55
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
6 days ago
Dennis
• 0
0
votes
1
reply
91
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 2 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
Lucie
• 0
8
votes
23
replies
690
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 5 days ago by
Robert Castelo
★ 3.2k • written 6 days ago by
Bine
▴ 40
0
votes
1
reply
95
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 6 days ago by
ATpoint
★ 4.0k • written 8 days ago by
Merav
• 0
0
votes
2
replies
166
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 6 days ago by
Michael Love
41k • written 11 days ago by
nhaus
▴ 30
0
votes
1
reply
113
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Adelaide
• 0
0
votes
2
replies
202
views
Regressing out batch effects
DESeq2
updated 6 days ago by
Michael Love
41k • written 12 days ago by
kys91240
• 0
5
votes
6
replies
343
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 3 days ago by
ATpoint
★ 4.0k • written 7 days ago by
nhaus
▴ 30
0
votes
1
reply
108
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
zh9118
• 0
45,526 results • Page
1 of 911
Recent ...
Replies
Comment: DEG with low counts
by
Rajat
• 0
Dear Dr. Michael Thanks for you quick reply. I appreciate it. Attached is the plotcounts for one gene. I am experiencing like this in oth…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for your guide! I check my data as you said there is no difference in my data. This is the MDS plot at genes l…
Comment: How to correct for known and surrogate variables in DESeq2?
by
Michael Love
41k
To question 3: if you model technical variation using only ~group vs ~1, then it will be correlated with known technical variables, which y…
Answer: flowStats Search Error
by
shepherl
3.8k
We are aware of an issue with bioconductor.org search and are investigating. We apologize for an inconvenience this is causing.
Comment: How to correct for known and surrogate variables in DESeq2?
by
nhaus
▴ 30
Hey Crystal, did you end up getting advice? I am facing the exact same questions that you are having right now. Would be very grateful if y…
Votes
Answer: Light difference when using coef vs omit a group when compare 3 groups.
C: Add new columns to DESeqResults from text file by matching rownames.
Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
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