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3
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6
replies
1.9k
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Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
3.1 years ago
mohammedtoufiq91
▴ 10
2
votes
5
replies
2.9k
views
ComplexHeatmap - z-score color coding failed
heatmaps
ComplexHeatmap
3.1 years ago
Katharina
• 0
0
votes
2
replies
1.4k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment
Biostrings
updated 15 months ago by
rohitsatyam102
▴ 20 • written 3.1 years ago by
潘晓光
• 0
6
votes
6
replies
3.1k
views
limma plotMDS - logFC inverted?
limma
MultidimensionalScaling
updated 16 months ago by
James W. MacDonald
68k • written 3.1 years ago by
Katharina
• 0
0
votes
1
reply
1.7k
views
minfi read.metharray.sheet error
minfi
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
jasmine_chappell
• 0
0
votes
1
reply
1.2k
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Laia
▴ 10
0
votes
1
reply
1.6k
views
rma normalization using microarray data
cdf
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Charmy
• 0
0
votes
0
replies
800
views
Updating 16S training set with LearnTaxa
DECIPHER
3.1 years ago
Connor
• 0
1
vote
1
reply
745
views
Limma, Log2FC and pvalue changing depending on the order of the samples.
limma
updated 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
eiudkann
• 0
0
votes
0
replies
1.4k
views
Job:
Job as a bioinformatician in Hamburg, Germany
DimensionReduction
SingleCellData
multiomics
MachineLearning
3.1 years ago
Diego's
• 0
0
votes
2
replies
1.4k
views
Results analysis of differential gene expression using DESeq2 package
RnaSeqSampleSize
statistics
DESeq2
updated 3.1 years ago by
swbarnes2
★ 1.4k • written 3.1 years ago by
N
• 0
0
votes
4
replies
1.1k
views
what could be the source of this erro
DrugVsDiseasedata
written 3.1 years ago by
Abdul
• 0
0
votes
0
replies
922
views
I/O Error in install 'EnsDb.Hsapiens.v75' on a CentOS platform
EnsDb.Hsapiens.v75
3.1 years ago
hjh811638667
• 0
0
votes
1
reply
1.8k
views
DGE genes are not available in GSEA
dge
gsea
updated 3.1 years ago by
Guido Hooiveld
★ 4.1k • written 3.1 years ago by
Lawrence
• 0
0
votes
3
replies
1.6k
views
A look inside annotation packages
Annotation
3.1 years ago
Ed Siefker
▴ 230
4
votes
6
replies
1.9k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
3.1 years ago
Abdul
▴ 20
0
votes
1
reply
1.1k
views
Job:
'Omics data analyst for HPCBio, University of Illinois
SingleCell
rnaseq
methylationArrayAnalysis
Spatial
written 3.1 years ago by
Jenny Drnevich
★ 2.0k
7
votes
6
replies
5.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
nhaus
▴ 70
0
votes
2
replies
1.3k
views
How to filter for counts in different columns
DESeq2
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Konstantinos
• 0
3
votes
2
replies
9.2k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 3.1 years ago by
snijesh
▴ 200 • written 8.1 years ago by
p_donchev84
• 0
0
votes
2
replies
4.7k
views
Error in UseMethod("rescale")
clusterProfiler
updated 3.1 years ago by
Guido Hooiveld
★ 4.1k • written 3.1 years ago by
vvelagal
• 0
1
vote
6
replies
6.6k
views
KEGG enrichment analysis for non model organism
RNAseq123
3.1 years ago
afsanarupa1
• 0
2
votes
3
replies
3.2k
views
How to use a specific Bioconductor version in custom Dockerfile
singularity
ensemblVEP
docker
3.1 years ago
jtaylor-predicine
• 0
0
votes
1
reply
1.5k
views
Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boundaries of non-circular sequence "chr2"
HiCDCPlus
BSgenome.Hsapiens.UCSC.hg38
updated 2.6 years ago by
merve.sahn
• 0 • written 3.1 years ago by
Yue
• 0
1
vote
1
reply
1.3k
views
In readLines(csvfile)
pipeline
testdata
ChAMP
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
luisfranciscoteves
• 0
0
votes
5
replies
2.1k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
teetee
• 0
0
votes
2
replies
1.4k
views
abs() error in rstudio
Bioconductor
BiocManager
abs()
Bioinformatics
written 3.2 years ago by
sue
• 0
0
votes
2
replies
1.2k
views
Does the knock down cause transcriptome-wide differences in isoform usage for Pac-Bio data?
pacbio
isoform
written 3.2 years ago by
lhaiyan3
• 0
5
votes
6
replies
3.7k
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM
filterByExpr
edgeR
histogram
rowsums
3.1 years ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
1.0k
views
Limma-voom - Timepoint by timepoint comparison in timecourse experiment
limma
written 3.2 years ago by
rina
▴ 30
0
votes
2
replies
1.2k
views
could not find function "get_known_signatures"
MutationalPatterns
updated 3.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.1 years ago by
anton.kratz
▴ 60
2
votes
2
replies
1.3k
views
HMP1-II Metagenomic Data
MicrobiomeData
curatedMetagenomicData
3.2 years ago • updated 3.1 years ago
Pauline
▴ 20
0
votes
3
replies
1.8k
views
Problem with multiple sequence alignment using AlignSeqs
R
dada2
DECIPHER
updated 3.1 years ago by
Erik Wright
▴ 150 • written 3.1 years ago by
Nelli
• 0
0
votes
3
replies
1.6k
views
question about removing both known and unknown confounders
DESeq2
RUVSeq
updated 3.1 years ago by
Michael Love
43k • written 3.2 years ago by
Lisa
• 0
0
votes
2
replies
898
views
checkFullRank(modelMatrix) while neither factor can be predicted from each other.
DESeq2
updated 3.1 years ago by
swbarnes2
★ 1.4k • written 3.1 years ago by
TzuChiao
▴ 10
1
vote
13
replies
3.1k
views
Deseq2 , result() taking too long > 3hrs
DESeq2
updated 2.9 years ago by
jon50250
• 0 • written 3.1 years ago by
Nidhi
• 0
1
vote
2
replies
1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
3.1 years ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
4.0k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads
STAR
featureCounts
updated 3.1 years ago by
swbarnes2
★ 1.4k • written 3.1 years ago by
lalala
• 0
0
votes
0
replies
857
views
RUVg for SNAP-ChIP ?
RUVSeq
3.1 years ago
Bogdan
▴ 670
4
votes
8
replies
3.6k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 2.7 years ago by
Gordon Smyth
53k • written 3.2 years ago by
Sabiha
▴ 20
1
vote
2
replies
1.3k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
3.2 years ago
mohammedtoufiq91
▴ 10
2
votes
9
replies
3.2k
views
countToFPKM and featureLength
countToFPKM
updated 3.1 years ago by
swbarnes2
★ 1.4k • written 3.2 years ago by
Morris
▴ 10
0
votes
0
replies
569
views
RNA seq analysis
RNASeq
3.2 years ago
lesseyl
• 0
11
votes
17
replies
4.2k
views
SV4Vectors DataFrame bug with haven_labelled data
S4Vectors
DataFrame
haven_labelled
haven
updated 3.1 years ago by
Danny Smith
▴ 20 • written 3.2 years ago by
Daniel E. Weeks
▴ 30
1
vote
3
replies
1.0k
views
DESeq2 on multiple sample groups
DESeq2
written 3.2 years ago by
grsyhhsb
• 0
3
votes
7
replies
3.8k
views
Is it possible to convert "DESeq2's normalized counts" to "DEGs"?
DESeq2
raw
updated 3.2 years ago by
swbarnes2
★ 1.4k • written 3.2 years ago by
Hicham
▴ 10
0
votes
2
replies
1.5k
views
Differentially expression analysis of orthologous genes between two species
DESeq2
tximport
3.2 years ago
Konstantinos
• 0
0
votes
2
replies
853
views
Setting up contrasts within a dataset within conditions (across different genotype) and across conditions (for the same genotype)
DESeq2
3.2 years ago • updated 3.1 years ago
nrama
• 0
0
votes
1
reply
885
views
HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 annotation
HiC-DC+
HiCDCPlus
updated 2.6 years ago by
merve.sahn
• 0 • written 3.2 years ago by
Yue
• 0
0
votes
3
replies
2.9k
views
Cannot download flowUtils package from Bioconductor 3.16
Bioconductor
flowUtils
updated 3.2 years ago by
Mike Smith
★ 6.6k • written 3.2 years ago by
Zoya
• 0
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
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 …
Votes
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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