Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
0
votes
0
replies
14
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
4 hours ago
rocanja
▴ 60
0
votes
0
replies
13
views
Error in msaFun Cannot open input file. No alignment!
msa
11 hours ago
Kamil Slowikowski
▴ 30
0
votes
0
replies
22
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
13 hours ago
Julie
• 0
0
votes
0
replies
19
views
Help with Complex DESeq2 Design
DESeq2
13 hours ago
kelsey.beavers
• 0
1
vote
0
replies
40
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
19 hours ago
andrebolerbarros
▴ 30
4
votes
2
replies
67
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
20 hours ago • updated 10 hours ago
Georg
• 0
1
vote
3
replies
92
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 7 hours ago by
Gordon Smyth
50k • written 21 hours ago by
JKim
• 0
2
votes
2
replies
109
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
1 day ago • updated 19 hours ago
Eva
▴ 10
0
votes
1
reply
38
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 1 day ago by
Michael Love
41k • written 1 day ago by
rahaf.nazzal9
• 0
0
votes
3
replies
84
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
updated just now by
James W. MacDonald
65k • written 1 day ago by
Efra
• 0
0
votes
1
reply
45
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Yuqin
• 0
1
vote
1
reply
67
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Emma
• 0
3
votes
3
replies
104
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 4 hours ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
0
votes
1
reply
77
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium
genom
linka
GenomicDistributionsData
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
zoheir.alayash
• 0
0
votes
1
reply
83
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 2 days ago by
Gordon Smyth
50k • written 4 days ago by
Gerhard Thallinger
▴ 180
2
votes
2
replies
114
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
4 days ago • updated 2 days ago
feather-W
• 0
0
votes
2
replies
156
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
z_bahari
• 0
2
votes
2
replies
153
views
between lane normalization upper quantile
EDASeq
edgeR
4 days ago • updated 1 day ago
elesofi
• 0
0
votes
1
reply
74
views
problem with ClusterRepro function
WGCNA
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
Antonio.Aubry
• 0
0
votes
4
replies
301
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
Jad
• 0
2
votes
2
replies
141
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 days ago
Sabiha
▴ 20
0
votes
2
replies
126
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 days ago • updated 4 days ago
kcarey
• 0
0
votes
6
replies
254
views
DESeq2 filtering vs edgeR filtering
DESeq2
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
fr8712ca-s
• 0
0
votes
2
replies
189
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 5 days ago by
Michael Love
41k • written 6 days ago by
gglatzer
• 0
0
votes
2
replies
140
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 days ago • updated 5 days ago
Sam
▴ 10
2
votes
1
reply
153
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 6 days ago by
ATpoint
★ 3.9k • written 6 days ago by
hemantcnaik
• 0
1
vote
1
reply
132
views
i'm not getting any differentially expressed genes.
DESeq2
updated 6 days ago by
ATpoint
★ 3.9k • written 7 days ago by
Marilyn
• 0
0
votes
1
reply
120
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 7 days ago by
BioinfoMug
• 0
0
votes
1
reply
110
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 days ago • updated 2 days ago
red_bricks
▴ 50
0
votes
0
replies
72
views
FELLA plotGraph function won't change the legend
FELLA
7 days ago
yuhang
• 0
0
votes
0
replies
73
views
medips-output
ngsReports
MEDIPS
7 days ago
subhiksha
• 0
0
votes
0
replies
62
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
7 days ago
bocsci11
• 0
0
votes
0
replies
67
views
The graphical interface of FELLA doesn't work
FELLA
8 days ago
yuhang
• 0
0
votes
0
replies
80
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
8 days ago
jean-christophe.helbling
• 0
0
votes
1
reply
90
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 7 days ago by
James W. MacDonald
65k • written 8 days ago by
maltethodberg
▴ 170
0
votes
4
replies
183
views
Error in classify_gene_pairs
syntenet
doubletrouble
8 days ago • updated 7 days ago
hfyuan2016
• 0
1
vote
1
reply
138
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 8 days ago by
ATpoint
★ 3.9k • written 8 days ago by
synat.keam
• 0
0
votes
0
replies
90
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
11 days ago
Henry
• 0
1
vote
5
replies
263
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
11 days ago • updated 1 day ago
Gerhard Thallinger
▴ 180
0
votes
1
reply
131
views
Rcpp compilation error
Release
Rcpp
updated 11 days ago by
ATpoint
★ 3.9k • written 11 days ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
90
views
Rain error: invalid annotation of time points
rain
11 days ago
mpuli011
• 0
0
votes
2
replies
245
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
11 days ago • updated 10 days ago
Viktor Thiel
• 0
0
votes
0
replies
81
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
11 days ago
Felix
• 0
0
votes
1
reply
110
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 11 days ago by
ATpoint
★ 3.9k • written 11 days ago by
daiane.hemerichbrennan
• 0
1
vote
2
replies
170
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
11 days ago
thomas
• 0
1
vote
1
reply
129
views
Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 11 days ago by
James W. MacDonald
65k • written 12 days ago by
ronin
• 0
0
votes
8
replies
258
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
12 days ago • updated 11 days ago
michelafrancesconi8
• 0
0
votes
0
replies
90
views
News:
Join BOC Sciences at Drug Discovery Chemistry 2024
DFP
12 days ago
cv.jam.zhxf17875
• 0
0
votes
1
reply
136
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 12 days ago by
ATpoint
★ 3.9k • written 12 days ago by
Sneha
• 0
0
votes
5
replies
250
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Lily Cheang
• 0
45,401 results • Page
1 of 909
Recent ...
Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
C: How to check that the reads in two fastq files are in the same order
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Awards
• All
Scholar
to
James W. MacDonald
65k
Scholar
to
Gordon Smyth
50k
Popular Question
to
rocanja
▴ 60
Popular Question
to
rproendo
▴ 20
Popular Question
to
Wolfgang RAFFELSBERGER
▴ 140
Locations
• All
Germany,
2 minutes ago
United States,
3 minutes ago
United States,
15 minutes ago
Jerusalem,
37 minutes ago
UPF, Barcelona, Spain,
40 minutes ago
Traffic: 661 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6