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59
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News:
TIDES USA 2024
flowBeads
7 days ago
bocsci11
• 0
0
votes
1
reply
111
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Brynn
• 0
0
votes
1
reply
115
views
Adding columns to DEXSeqResults object
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Clyde
• 0
0
votes
0
replies
76
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
8 days ago
Maliha Tabassum
• 0
1
vote
2
replies
110
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
8 days ago
Ana
• 0
0
votes
1
reply
98
views
what is the sampleFiles
chipseq
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
zhulin
• 0
0
votes
4
replies
148
views
flowStats Search Error
flowStats
updated 8 days ago by
shepherl
3.8k • written 9 days ago by
tholmes
• 0
0
votes
0
replies
76
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
9 days ago
Virangika
• 0
0
votes
0
replies
57
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
9 days ago
Henry
▴ 10
0
votes
3
replies
174
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
292
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
9 days ago • updated 8 days ago
daniel.carbajo
• 0
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 5 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
1
vote
2
replies
354
views
GSVA error
GSVA
10 days ago • updated 9 days ago
Alex
• 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 11 days ago by
Sahar
• 0
1
vote
1
reply
160
views
Differentially expressed genes in monocle pseudotime
monocle
updated 8 days ago by
Gordon Smyth
50k • written 11 days ago by
kthapa
• 0
0
votes
1
reply
117
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 8 days ago by
James W. MacDonald
65k • written 11 days ago by
tian.liu0720
• 0
2
votes
2
replies
144
views
[DiffBind] Obtaining normalization factors
DiffBind
12 days ago • updated 8 days ago
Henry
▴ 10
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
12 days ago • updated 11 days ago
hemantcnaik
• 0
0
votes
1
reply
117
views
Bioinformatics student
Des
DESeq2
updated 12 days ago by
hemantcnaik
• 0 • written 12 days ago by
Sahar
• 0
2
votes
2
replies
166
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
12 days ago
julia_mcdonough
• 0
0
votes
0
replies
70
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
12 days ago
shepherl
3.8k
3
votes
3
replies
167
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
12 days ago • updated 6 days ago
jacques.imbert
• 0
2
votes
2
replies
146
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
12 days ago • updated 9 days ago
daniel.carbajo
• 0
0
votes
3
replies
221
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 6 days ago by
W. Evan Johnson
▴ 850 • written 12 days ago by
schlumbohm
• 0
0
votes
0
replies
73
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
12 days ago
Stevie Pederson
• 0
2
votes
2
replies
352
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
13 days ago • updated 12 days ago
Henry
▴ 10
0
votes
0
replies
82
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
13 days ago
communication
• 0
4
votes
8
replies
341
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 6 days ago by
Peter Hickey
▴ 740 • written 13 days ago by
Juan Higareda
• 0
3
votes
6
replies
230
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
13 days ago
nhaus
▴ 30
0
votes
1
reply
120
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 9 days ago by
kamryncole1963
• 0 • written 13 days ago by
Sara
• 0
0
votes
1
reply
155
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago
Shefali
• 0
1
vote
2
replies
217
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
5
votes
9
replies
853
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
14 days ago • updated 6 days ago
Chris
• 0
0
votes
0
replies
111
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
14 days ago
Eryn
• 0
0
votes
0
replies
76
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
14 days ago
Dennis
• 0
0
votes
1
reply
132
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 10 days ago by
Guido Hooiveld
★ 3.9k • written 14 days ago by
Lucie
• 0
0
votes
4
replies
199
views
Storing directories inside an ExperimentHub package?
ExperimentHub
14 days ago • updated 13 days ago
Tim Barry
• 0
8
votes
23
replies
845
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 13 days ago by
Robert Castelo
★ 3.3k • written 14 days ago by
Bine
▴ 40
1
vote
3
replies
320
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 9 days ago by
Gordon Smyth
50k • written 14 days ago by
Simran
• 0
0
votes
1
reply
129
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
zh9118
• 0
0
votes
1
reply
137
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 15 days ago by
Michael Love
41k • written 15 days ago by
Adelaide
• 0
5
votes
6
replies
392
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 11 days ago by
ATpoint
★ 4.0k • written 15 days ago by
nhaus
▴ 30
0
votes
0
replies
90
views
ggtree tip label position (depth)
ggtree
15 days ago • updated 14 days ago
Roope
• 0
1
vote
6
replies
454
views
GSVA on separate healthy and disease datasets
GSVA
updated 14 days ago by
James W. MacDonald
65k • written 15 days ago by
Lucy
▴ 60
2
votes
6
replies
342
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
16 days ago
Chris
• 0
0
votes
1
reply
119
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 14 days ago by
ATpoint
★ 4.0k • written 16 days ago by
Merav
• 0
0
votes
0
replies
120
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
16 days ago
arne.sahm
• 0
0
votes
0
replies
82
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
16 days ago
Wolfgang Huber
★ 13k
3
votes
3
replies
282
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 16 days ago by
Netanel
• 0
0
votes
1
reply
159
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
BCS12
• 0
1,748 results • Page
2 of 35
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
I am not sure how your comment helps here?
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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