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0
votes
0
replies
1.0k
views
Concatenating different runs from the same pool of barcoded CyTOF samples
batch effect
cytof
5.8 years ago
mikhael.manurung
▴ 280
1
vote
2
replies
1.8k
views
RNAseq analysis with edgeR-interaction terms and comparison within and between groups
edger
updated 5.8 years ago by
Gordon Smyth
53k • written 5.9 years ago by
erwagner2
• 0
4
votes
4
replies
2.5k
views
Issues loading a BAM file resulted from featurecounts
featurecount
rsubread
GenomicAlignments
5.9 years ago
Konstantinos Yeles
▴ 90
1
vote
2
replies
836
views
BATCH EFFECT OF AGE
deseq2
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
Matan G.
▴ 60
5
votes
10
replies
2.3k
views
tximport and stevia, how to build tx2gene without any reference genome
deseq2
annotation
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
bahmanik@msu.edu
▴ 60
0
votes
0
replies
792
views
MAIT metabolomics analysis error
mait
5.9 years ago
YL
• 0
2
votes
4
replies
1.9k
views
DESeq2 result extraction
deseq2
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
adR
▴ 40
0
votes
0
replies
534
views
DESeq2 analysis with scaled continues variables
normalization
5.9 years ago
adR
▴ 40
1
vote
1
reply
974
views
DESeq2 paired test (for most samples)
deseq2
paired
tumor vs normal
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
dagsbio
• 0
1
vote
9
replies
2.1k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 5.9 years ago by
Simon Anders
★ 3.8k • written 5.9 years ago by
megapode32559
• 0
7
votes
16
replies
5.3k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores
granges
phastCons100way.UCSC.hg38
r
rtracklayer
updated 14 months ago by
rania.alanany
• 0 • written 5.9 years ago by
Biologist
▴ 120
0
votes
1
reply
1.5k
views
can't library hgu133plus2cdf
hgu133plus2cdf
5.9 years ago
1142985358
• 0
0
votes
6
replies
947
views
Why so few genes are returned?
deseq2
updated 5.9 years ago by
Kevin Blighe
★ 4.0k • written 5.9 years ago by
megapode32559
• 0
0
votes
0
replies
959
views
Error on FindOptimalBinning function
bhc
error
5.9 years ago
pavel.granalacant
• 0
4
votes
2
replies
6.5k
views
DESeq2 Multiple Conditions: Do I need a "reference"?
deseq2
updated 5.9 years ago by
Kevin Blighe
★ 4.0k • written 5.9 years ago by
cnvspam
▴ 10
1
vote
2
replies
1.4k
views
The coordinate system problem about DiffBind output
diffbind
Rory Stark
coordinate
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
Guandong Shang
▴ 40
3
votes
2
replies
1.5k
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind
CPM
TMM
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
Guandong Shang
▴ 40
1
vote
2
replies
799
views
Diffbind- results different every time I run it
software error
DiffBind
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
francesca3
• 0
1
vote
1
reply
1.4k
views
DiffBind in depth explanation
DiffBind
PCA
Differential Analysis
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
jrp208
• 0
2
votes
3
replies
1.4k
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq
Paired design
Timecourse
Diagnosis
Covariates
updated 5.9 years ago by
Kevin Blighe
★ 4.0k • written 5.9 years ago by
ibrahim.akkouh
• 0
0
votes
0
replies
1.3k
views
WGCNA for Dose-Response RNA-Seq Data
wgcna
network analysis
5.9 years ago
jwilliamblamer
• 0
1
vote
3
replies
1.6k
views
Design DESeq2 with one or more continues variables
deseq2
5.9 years ago
adR
▴ 40
2
votes
2
replies
2.1k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db
KEGG
KEGGPATHNAME2ID
KEGGPATHID2EXTIT
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
tobias-messmer
▴ 20
6
votes
9
replies
6.0k
views
Centering and scaling numeric variables
deseq2
updated 5.9 years ago by
adR
▴ 40 • written 5.9 years ago by
MiKappa
▴ 30
0
votes
0
replies
1.3k
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
5.9 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
5
replies
2.7k
views
biomaRt getBM() returns nothing most of the times
biomaRt
getBM
updated 5.9 years ago by
swbarnes2
★ 1.4k • written 5.9 years ago by
laurenz.holcik
• 0
0
votes
4
replies
771
views
How to know what genes are differentially expression in DESeq2 simulation?
deseq2
updated 5.9 years ago by
Kevin Blighe
★ 4.0k • written 5.9 years ago by
megapode32559
• 0
2
votes
4
replies
3.7k
views
Quality control in SingleCellExperiment
SingleCellExperiment
scater
sce
quality control
updated 5.0 years ago by
1498554536
• 0 • written 5.9 years ago by
Linda
• 0
0
votes
1
reply
387
views
Choosing DESeq2 design
deseq2
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
zen
• 0
0
votes
1
reply
2.0k
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
Guillaume Robert
• 0
0
votes
6
replies
1.7k
views
tximport lose transcript names with Salmon bootstrap
salmon
tximport
bootstrap
updated 5.9 years ago by
julia.jefferson23
• 0 • written 5.9 years ago by
Cindy
• 0
1
vote
3
replies
1.2k
views
DE analysis outlier removal
deseq2
outlier
normalization
removal
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
knholm
• 0
0
votes
1
reply
745
views
TxDb.Hsapiens.UCSC.hg38.knownGene immunoglobulin
annotation
updated 5.9 years ago by
Hervé Pagès
16k • written 5.9 years ago by
ksasaki
• 0
0
votes
5
replies
3.1k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 9 months ago by
瑞宏
• 0 • written 5.9 years ago by
jashmore
• 0
0
votes
1
reply
2.0k
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR
MouseGastrulationData
updated 5.9 years ago by
Aaron Lun
★ 29k • written 5.9 years ago by
jma1991
▴ 70
1
vote
5
replies
2.1k
views
Gene Ontology analysis
ontology
edger
limma
ncbi
organism package
updated 5.9 years ago by
Gordon Smyth
53k • written 5.9 years ago by
babak.loghmani
▴ 20
1
vote
12
replies
2.4k
views
negative one "-1" values in index files using Rsubread
software error
rsubread
updated 5.9 years ago by
Yang Liao
▴ 450 • written 5.9 years ago by
peter.r.hoyt
• 0
0
votes
1
reply
917
views
DESeq dispersion parameter
deseq2
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
stephen.hartley
• 0
0
votes
2
replies
1.0k
views
phyloseq_to_deseq2 design strategy for multiple factors analysis (2 or more)
deseq2
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
pyveronneau71
• 0
2
votes
4
replies
1.6k
views
Joint pathway Analysis using both gene and metabolite data sets
data integration
gene
metabolite
5.9 years ago
emisecherre
• 0
5
votes
2
replies
1.8k
views
DESeq2 pairwise comparisons w/ 3 factors
deseq2
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
aharkey
▴ 10
0
votes
1
reply
612
views
DiffBind 2.10.0: Consensus peaks seems to miss 2/3 of original sample peaks
DiffBind
Consensus peak
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
rmendez
• 0
0
votes
2
replies
1.2k
views
DiffBind: error with dba.peakset()
DiffBind
Peakset
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
hkitano
• 0
1
vote
7
replies
3.8k
views
DiffBind: dealing with replicates
diffbind
chipseq
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
hkitano
• 0
8
votes
5
replies
4.5k
views
How to know if I should use voomWithQualityWeights() or not?
limma
RNA-Seq
voom
voomWithQualityWeights
edgeR
updated 5.9 years ago by
Gordon Smyth
53k • written 5.9 years ago by
pedrodcb
▴ 10
2
votes
4
replies
5.4k
views
How to get list of all GOIDs with all genes in each GO term?
go
annotation
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
theodore.killian
• 0
1
vote
1
reply
1.4k
views
Trouble using affy library
software error
R
microarray
affy
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
adam_casas
• 0
2
votes
1
reply
1.3k
views
MEDIPS - Error in MEDIPS.CpGenrich
MEDIPS
updated 5.9 years ago by
Lukas Chavez
▴ 570 • written 5.9 years ago by
gaurav4thareja
▴ 20
0
votes
6
replies
1.8k
views
Remove batch effect for DESeq2
deseq2
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
luongthang1908
• 0
3
votes
2
replies
1.4k
views
Does a specific bioconductor version constrain versions of non-bioconductor packages?
reproducibility
versions
installing
base-r
updated 5.9 years ago by
Mike Smith
★ 6.6k • written 5.9 years ago by
Yannick Wurm
▴ 40
46,730 results • Page
175 of 935
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Comment: Bile acid analysis with limpa
by
ATpoint
★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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