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0
votes
0
replies
11
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
2 hours ago
rocanja
▴ 60
1
vote
3
replies
2.8k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 4 hours ago by
snijesh
▴ 20 • written 6.4 years ago by
Ramiro Magno
▴ 100
0
votes
0
replies
12
views
Error in msaFun Cannot open input file. No alignment!
msa
9 hours ago
Kamil Slowikowski
▴ 30
1
vote
3
replies
82
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 5 hours ago by
Gordon Smyth
50k • written 20 hours ago by
JKim
• 0
0
votes
0
replies
22
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
11 hours ago
Julie
• 0
0
votes
0
replies
18
views
Help with Complex DESeq2 Design
DESeq2
12 hours ago
kelsey.beavers
• 0
4
votes
2
replies
65
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
18 hours ago • updated 8 hours ago
Georg
• 0
1
vote
0
replies
38
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
17 hours ago
andrebolerbarros
▴ 30
3
votes
15
replies
2.5k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
8 months ago • updated 20 hours ago
shepherl
3.8k
2
votes
2
replies
106
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
22 hours ago • updated 17 hours ago
Eva
▴ 10
0
votes
2
replies
76
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
1 day ago • updated 7 hours ago
Efra
• 0
1
vote
1
reply
66
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 23 hours ago by
Michael Love
41k • written 1 day ago by
Emma
• 0
0
votes
1
reply
38
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 23 hours ago by
Michael Love
41k • written 1 day ago by
rahaf.nazzal9
• 0
0
votes
1
reply
44
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
7
replies
1.0k
views
enrichGOgradient color change
clusterProfiler
updated 1 day ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
inna.gur
• 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
3
replies
100
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 2 hours ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
0
votes
2
replies
155
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
z_bahari
• 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
2
votes
2
replies
113
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
4 days ago • updated 2 days ago
feather-W
• 0
0
votes
1
reply
82
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
153
views
between lane normalization upper quantile
EDASeq
edgeR
4 days ago • updated 1 day ago
elesofi
• 0
2
votes
3
replies
2.0k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 2 days ago by
ATpoint
★ 3.9k • written 23 months ago by
liqidong52
▴ 20
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
2
replies
188
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 4 days ago by
Michael Love
41k • written 6 days ago by
gglatzer
• 0
0
votes
4
replies
299
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
140
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 days ago • updated 4 days ago
Sabiha
▴ 20
0
votes
6
replies
253
views
DESeq2 filtering vs edgeR filtering
DESeq2
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
fr8712ca-s
• 0
0
votes
2
replies
139
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 days ago • updated 5 days ago
Sam
▴ 10
0
votes
2
replies
125
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 days ago • updated 4 days ago
kcarey
• 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 6 days ago by
Marilyn
• 0
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
0
votes
1
reply
119
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
1
reply
180
views
Syntenet error in infer_syntenet() Error in blast_list[[1]] : subscript out of bounds
syntenet
updated 7 days ago by
Fabricio Almeida-Silva
▴ 40 • written 6 weeks ago by
Sujeevan
• 0
0
votes
1
reply
208
views
question about data processing for syntenet
syntenet
updated 7 days ago by
Fabricio Almeida-Silva
▴ 40 • written 10 weeks ago by
Sujeevan
• 0
0
votes
2
replies
219
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
18 days ago • updated 6 days ago
shepherl
3.8k
0
votes
4
replies
182
views
Error in classify_gene_pairs
syntenet
doubletrouble
8 days ago • updated 7 days ago
hfyuan2016
• 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
0
replies
66
views
The graphical interface of FELLA doesn't work
FELLA
7 days ago
yuhang
• 0
0
votes
0
replies
79
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
8 days ago
jean-christophe.helbling
• 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
3
replies
276
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 6 weeks ago by
pl23
• 0
0
votes
2
replies
244
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
11 days ago • updated 9 days ago
Viktor Thiel
• 0
0
votes
0
replies
90
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
11 days ago
Henry
• 0
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
45,401 results • Page
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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: 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: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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