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package goseq seems to be not available on the latest version of R
goseq
10 minutes ago
Patrycja
• 0
2
votes
2
replies
40
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 54 minutes ago by
Michael Love
41k • written 1 hour ago by
Reza
• 0
0
votes
0
replies
12
views
Handling multiple differential expression comparisons
DESeq2
2 hours ago
Zainab
• 0
0
votes
0
replies
13
views
dba.plotProfile() plotting and interpretation
DiffBind
2 hours ago
Henry
▴ 10
0
votes
1
reply
70
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 21 hours ago by
Gordon Smyth
50k • written 1 day ago by
z_bahari
• 0
0
votes
1
reply
68
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 21 hours ago by
Gordon Smyth
50k • written 1 day ago by
c53aba27
• 0
0
votes
1
reply
157
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 16 hours ago by
Gordon Smyth
50k • written 1 day ago by
gene_bioconductor
▴ 10
0
votes
5
replies
115
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 6 hours ago by
James W. MacDonald
65k • written 23 hours ago by
arfranco
▴ 130
0
votes
0
replies
22
views
flowStats for CyTOF
flowStats
1 day ago
tholmes
• 0
0
votes
2
replies
65
views
DESeq2 v1.35.0
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Espresso
• 0
0
votes
0
replies
31
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
1 day ago
yvonneh
• 0
0
votes
0
replies
25
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
1 day ago
Ian D.
▴ 70
0
votes
1
reply
38
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 1 day ago by
4r-rtg
• 0
0
votes
2
replies
99
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
2 days ago • updated 1 day ago
Ian D.
▴ 70
0
votes
2
replies
95
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 20 hours ago
kcarey
• 0
0
votes
3
replies
102
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
james.zhang20
• 0
0
votes
1
reply
108
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
angelathuynh5
• 0
3
votes
0
replies
45
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
1 day ago
shepherl
3.9k
0
votes
0
replies
64
views
Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 1 day ago
Chris
• 0
0
votes
3
replies
124
views
Store output of matchPWM()
biostrings
Biostrings
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
mat149
▴ 70
0
votes
3
replies
223
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
HAK
• 0
0
votes
2
replies
200
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
2 days ago • updated 1 day ago
Yveto
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 2 days ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
211
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
3
votes
4
replies
179
views
Help with error using camera() in limma
CAMERA
limma
3 days ago
Chris
• 0
1
vote
1
reply
87
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
marcusn
• 0
0
votes
2
replies
102
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
3 days ago • updated 10 hours ago
Aurora
• 0
0
votes
1
reply
89
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
Agung
• 0
0
votes
0
replies
48
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
3 days ago
Maria Doyle
▴ 70
0
votes
1
reply
66
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 3 days ago by
shepherl
3.9k • written 3 days ago by
bounlu
• 0
0
votes
1
reply
88
views
putting my own expression data in deseq2
DESeq2
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
Dev
• 0
2
votes
2
replies
172
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
4 days ago • updated 3 days ago
Chris
• 0
0
votes
3
replies
214
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 3 days ago by
James W. MacDonald
65k • written 4 days ago by
SSSJec
• 0
0
votes
0
replies
58
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
4 days ago
Chris
• 0
3
votes
3
replies
200
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
bioinf
▴ 10
1
vote
1
reply
109
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by
Leo Lahti
▴ 40 • written 7 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
188
views
PCA plot suggestions
DESeq2
PCAtools
updated 7 days ago by
Michael Love
41k • written 8 days ago by
Aaliya
• 0
1
vote
3
replies
194
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 7 days ago by
Michael Love
41k • written 8 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
121
views
ATACseq merge peaks
DiffBind
updated 7 days ago by
ATpoint
★ 4.1k • written 9 days ago by
Shloka
• 0
1
vote
1
reply
155
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 7 days ago by
Gordon Smyth
50k • written 11 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
299
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
8 days ago • updated 7 days ago
pl23
• 0
2
votes
9
replies
352
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
Alexandre
• 0
0
votes
0
replies
93
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
8 days ago • updated 11 hours ago
glaciya2018
• 0
1
vote
2
replies
143
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
9 days ago • updated 8 days ago
ATpoint
★ 4.1k
0
votes
1
reply
138
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 8 days ago by
Michael Love
41k • written 9 days ago by
kcarey
• 0
0
votes
0
replies
75
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
9 days ago • updated 4 days ago
Sara
• 0
2
votes
5
replies
244
views
get BM error
ensembldb
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
Fara
• 0
2
votes
5
replies
220
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 8 days ago by
James W. MacDonald
65k • written 9 days ago by
bandconductor
• 0
0
votes
0
replies
76
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
9 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
205
views
Different Shrunk Log2FC according with reference
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
1,745 results • Page
1 of 35
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Votes
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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