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3
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15
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2.6k
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 10 days ago
shepherl
3.8k
2
votes
2
replies
186
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
10 days ago
Eva
▴ 10
0
votes
4
replies
305
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
10 days ago • updated 3 days ago
Efra
• 0
1
vote
1
reply
123
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 10 days ago by
Michael Love
41k • written 11 days ago by
Emma
• 0
0
votes
1
reply
102
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 10 days ago by
Michael Love
41k • written 10 days ago by
rahaf.nazzal9
• 0
0
votes
1
reply
122
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 11 days ago by
Michael Love
41k • written 11 days ago by
Yuqin
• 0
1
vote
7
replies
1.1k
views
enrichGOgradient color change
clusterProfiler
updated 11 days ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
inna.gur
• 0
1
vote
5
replies
333
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
21 days ago • updated 11 days ago
Gerhard Thallinger
▴ 180
4
votes
7
replies
328
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Amit
• 0
0
votes
2
replies
213
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
z_bahari
• 0
1
vote
1
reply
139
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium
genom
linka
GenomicDistributionsData
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
zoheir.alayash
▴ 10
2
votes
2
replies
164
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
13 days ago • updated 12 days ago
feather-W
• 0
0
votes
1
reply
129
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
Gerhard Thallinger
▴ 180
2
votes
2
replies
199
views
between lane normalization upper quantile
EDASeq
edgeR
14 days ago • updated 10 days ago
elesofi
• 0
2
votes
3
replies
2.1k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 12 days ago by
ATpoint
★ 4.0k • written 24 months ago by
liqidong52
▴ 20
0
votes
1
reply
131
views
problem with ClusterRepro function
WGCNA
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Antonio.Aubry
• 0
0
votes
2
replies
249
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 16 days ago by
gglatzer
• 0
0
votes
4
replies
356
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 14 days ago by
Michael Love
41k • written 15 days ago by
Jad
• 0
2
votes
2
replies
191
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
15 days ago • updated 14 days ago
Sabiha
▴ 20
0
votes
7
replies
342
views
DESeq2 filtering vs edgeR filtering
DESeq2
15 days ago • updated 2 days ago
fr8712ca-s
• 0
0
votes
2
replies
176
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
16 days ago • updated 15 days ago
Sam
▴ 10
0
votes
2
replies
166
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
15 days ago • updated 14 days ago
kcarey
• 0
1
vote
1
reply
167
views
i'm not getting any differentially expressed genes.
DESeq2
updated 16 days ago by
ATpoint
★ 4.0k • written 16 days ago by
Marilyn
• 0
2
votes
1
reply
193
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 16 days ago by
ATpoint
★ 4.0k • written 16 days ago by
hemantcnaik
• 0
0
votes
1
reply
166
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 17 days ago by
BioinfoMug
• 0
0
votes
1
reply
145
views
Exact same results in Diffbind with different normalization methods
DiffBind
17 days ago • updated 12 days ago
red_bricks
▴ 50
0
votes
0
replies
102
views
FELLA plotGraph function won't change the legend
FELLA
17 days ago
yuhang
• 0
0
votes
0
replies
101
views
medips-output
ngsReports
MEDIPS
17 days ago
subhiksha
• 0
0
votes
0
replies
98
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
17 days ago
bocsci11
• 0
0
votes
1
reply
211
views
Syntenet error in infer_syntenet() Error in blast_list[[1]] : subscript out of bounds
syntenet
updated 17 days ago by
Fabricio Almeida-Silva
▴ 40 • written 8 weeks ago by
Sujeevan
• 0
0
votes
1
reply
236
views
question about data processing for syntenet
syntenet
updated 17 days ago by
Fabricio Almeida-Silva
▴ 40 • written 11 weeks ago by
Sujeevan
• 0
0
votes
2
replies
266
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
28 days ago • updated 16 days ago
shepherl
3.8k
0
votes
4
replies
217
views
Error in classify_gene_pairs
syntenet
doubletrouble
18 days ago • updated 17 days ago
hfyuan2016
• 0
0
votes
1
reply
108
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
maltethodberg
▴ 170
0
votes
0
replies
87
views
The graphical interface of FELLA doesn't work
FELLA
17 days ago
yuhang
• 0
0
votes
0
replies
95
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
17 days ago
jean-christophe.helbling
• 0
1
vote
1
reply
162
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 18 days ago by
ATpoint
★ 4.0k • written 18 days ago by
synat.keam
• 0
0
votes
3
replies
307
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 8 weeks ago by
pl23
• 0
0
votes
2
replies
273
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
21 days ago • updated 19 days ago
Viktor Thiel
• 0
0
votes
0
replies
111
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
21 days ago
Henry
• 0
0
votes
1
reply
153
views
Rcpp compilation error
Release
Rcpp
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
113
views
Rain error: invalid annotation of time points
rain
21 days ago
mpuli011
• 0
0
votes
0
replies
104
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
21 days ago
Felix
• 0
0
votes
1
reply
138
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
daiane.hemerichbrennan
• 0
1
vote
2
replies
187
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
21 days ago
thomas
• 0
1
vote
1
reply
144
views
Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
ronin
• 0
0
votes
8
replies
296
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
21 days ago
michelafrancesconi8
• 0
0
votes
1
reply
151
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 22 days ago by
ATpoint
★ 4.0k • written 22 days ago by
Sneha
• 0
0
votes
0
replies
111
views
News:
Join BOC Sciences at Drug Discovery Chemistry 2024
DFP
22 days ago
cv.jam.zhxf17875
• 0
0
votes
6
replies
325
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
22 days ago • updated 3 days ago
Lily Cheang
• 0
45,441 results • Page
2 of 909
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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James W. MacDonald
65k
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50k
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