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Views
Votes
2
votes
3
replies
379
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
4 weeks ago • updated 29 days ago
jbgnielson
• 0
0
votes
1
reply
144
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
23 days ago • updated 2 days ago
shepherl
3.8k
0
votes
1
reply
144
views
few significant genes from DESeq2 analysis
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Ming
• 0
0
votes
3
replies
556
views
diffbind analyze for wheat
DiffBind
updated 29 days ago by
Igor
• 0 • written 6 months ago by
zgyu12
• 0
1
vote
5
replies
474
views
Duplicated expression values?
depmap_copyNumber()
depmap
written 5 months ago by
davi.vuko
• 0
5
votes
8
replies
1.1k
views
Batch correction and repeated measures
RUVSeq
sva
limma
6 months ago • updated 7 days ago
Jonathan
▴ 10
0
votes
2
replies
133
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
8 days ago • updated 7 days ago
kcarey
• 0
2
votes
5
replies
1.2k
views
Downloading count matrix for full recount3 dataset
recount3
updated 10 days ago by
Leonardo Collado Torres
★ 1.0k • written 2.7 years ago by
Ben
• 0
0
votes
11
replies
586
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
mico
• 0
0
votes
1
reply
135
views
Matrix multiplication error to estimate telomere length
methylclockData
minfi
methylclock
minfidata
updated 29 days ago by
James W. MacDonald
65k • written 4 weeks ago by
sharangiiv
• 0
0
votes
3
replies
1.3k
views
Error in ImportRData
dplyr
IsoformSwitchAnalyzeR
written 11 months ago by
ramon.dslps
• 0
1
vote
1
reply
122
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
4
votes
3
replies
164
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 10 days ago by
Georg
• 0
7
votes
6
replies
326
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Amit
• 0
0
votes
1
reply
171
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 24 days ago by
Gordon Smyth
50k • written 25 days ago by
Fabian
• 0
1
vote
1
reply
166
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
0
votes
2
replies
148
views
arm64 Update to flowWorkspace (4.14.2)
flowWorkspace
28 days ago
rgong1
• 0
0
votes
1
reply
88
views
collapseReplicates dimension error
DESeq2
Dese
updated 2 days ago by
Michael Love
41k • written 6 days ago by
Léa
• 0
0
votes
8
replies
294
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
21 days ago
michelafrancesconi8
• 0
0
votes
1
reply
101
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 10 days ago by
Michael Love
41k • written 10 days ago by
rahaf.nazzal9
• 0
1
vote
4
replies
265
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
28 days ago • updated 27 days ago
hmillike
• 0
1
vote
1
reply
143
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
2
votes
1
reply
191
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
4
votes
7
replies
613
views
DESeq2 unable to handle large count values
DESeq2
updated 9 days ago by
Michael Love
41k • written 4 months ago by
robennet
• 0
0
votes
3
replies
216
views
impute.knn produces different results based on matrix order
impute
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
Tamara
• 0
2
votes
3
replies
137
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 2 days ago by
Wei Shi
★ 3.6k • written 3 days ago by
thomas.heigl.ibk
• 0
0
votes
7
replies
575
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 27 days ago by
danalvoronov
▴ 10 • written 4 months ago by
jfmay
• 0
0
votes
1
reply
191
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2
pheatmap
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
zhangaimei
• 0
1
vote
2
replies
185
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
21 days ago
thomas
• 0
0
votes
1
reply
184
views
ExactTest vs QLFTest
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 29 days ago by
fr8712ca-s
• 0
0
votes
1
reply
30
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
4 hours ago • updated 3 hours ago
Faisal
• 0
1
vote
1
reply
136
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
0
votes
2
replies
136
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
9 days ago • updated 8 days ago
rocanja
▴ 60
0
votes
2
replies
1.0k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 9 days ago by
william
• 0 • written 17 months ago by
Maria Doyle
▴ 70
0
votes
1
reply
120
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 10 days ago by
Michael Love
41k • written 11 days ago by
Yuqin
• 0
1
vote
2
replies
134
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
3
votes
5
replies
543
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 24 days ago by
Michael Love
41k • written 4 weeks ago by
sap275
▴ 10
0
votes
10
replies
730
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
4 months ago • updated 27 days ago
ScafioRuo
• 0
4
votes
7
replies
324
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Amit
• 0
2
votes
3
replies
218
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 days ago by
Gordon Smyth
50k • written 10 days ago by
JKim
• 0
0
votes
3
replies
535
views
SingleR Label.Ont
SingleR
written 6 months ago by
saeed.khalili
• 0
0
votes
4
replies
215
views
Error in classify_gene_pairs
syntenet
doubletrouble
17 days ago
hfyuan2016
• 0
0
votes
6
replies
324
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
22 days ago • updated 3 days ago
Lily Cheang
• 0
0
votes
2
replies
1.4k
views
DE genes over time with DESeq2
deseq2
timecourse
design and contrast matrix
updated 21 days ago by
ta_awwad
▴ 10 • written 8.4 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
1
reply
160
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.0k • written 18 days ago by
synat.keam
• 0
4
votes
4
replies
1.0k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 13 days ago by
feather-W
• 0 • written 11 months ago by
Bernardo
▴ 10
1
vote
5
replies
995
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 24 days ago by
James W. MacDonald
65k • written 4 months ago by
rae.alshammari
▴ 10
1
vote
4
replies
234
views
DESeq2 Replicates
DESeq2
RNASeq
22 days ago
kcarey
• 0
0
votes
5
replies
124
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Jitendra
▴ 10
0
votes
3
replies
1.1k
views
Blacklist error in DiffBind
DiffBind
Blacklist
updated 19 days ago by
marram_wang
• 0 • written 16 months ago by
Romain
• 0
194 results • Page
2 of 4
Recent ...
Replies
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
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
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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