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15
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23
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5.3k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
20 months ago • updated 19 months ago
Chris
▴ 20
3
votes
6
replies
2.3k
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
written 20 months ago by
Fabian
• 0
0
votes
4
replies
1.0k
views
Minfi - estimatecellscount
min
minfi
updated 19 months ago by
James W. MacDonald
68k • written 20 months ago by
clacarion
• 0
0
votes
0
replies
649
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
20 months ago
feather-W
• 0
0
votes
0
replies
639
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
20 months ago
Ankit
▴ 20
0
votes
6
replies
1.3k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Faisal
• 0
1
vote
5
replies
1.2k
views
fgsea fork
fgsea
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
yimjohns
• 0
0
votes
1
reply
447
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Mikushi
• 0
0
votes
0
replies
617
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
20 months ago
Pierre Lindenbaum
▴ 10
2
votes
8
replies
1.4k
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Amit
• 0
0
votes
1
reply
693
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Karen
• 0
2
votes
4
replies
1.4k
views
PCA of different bacterial species
DESeq2
written 20 months ago by
Laura
▴ 10
1
vote
2
replies
762
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
20 months ago
Mj.A.
▴ 20
0
votes
1
reply
1.6k
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
21 months ago • updated 20 months ago
shepherl
4.2k
0
votes
2
replies
1.0k
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 20 months ago by
Michael Love
43k • written 20 months ago by
SG
• 0
2
votes
3
replies
1.0k
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 20 months ago by
Wei Shi
★ 3.6k • written 20 months ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
2.3k
views
From a DNAStringSet to a data.frame
Biostrings
20 months ago
ramiro.barrantes
▴ 10
0
votes
1
reply
608
views
collapseReplicates dimension error
DESeq2
Dese
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Léa
• 0
5
votes
25
replies
3.1k
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Jitendra
▴ 10
2
votes
4
replies
891
views
bioconductor emailing list
Bioconductor
20 months ago • updated 16 months ago
XFWu
• 0
3
votes
2
replies
787
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
20 months ago
Anita
▴ 10
3
votes
3
replies
2.4k
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 20 months ago by
alan.ocallaghan
▴ 160 • written 20 months ago by
Najla Abassi
• 0
2
votes
1
reply
1.0k
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
Dario Strbenac
★ 1.6k
0
votes
0
replies
793
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
20 months ago
gshweta95
• 0
0
votes
2
replies
1.9k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
20 months ago
Gordon
• 0
7
votes
6
replies
1.3k
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Amit
• 0
2
votes
2
replies
1.4k
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 20 months ago by
enee
▴ 10
0
votes
1
reply
1.2k
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
updated 5 months ago by
Ray
• 0 • written 20 months ago by
Maria Doyle
▴ 110
0
votes
1
reply
1.1k
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
scoops_streams_06
• 0
0
votes
0
replies
483
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
20 months ago
nromerov
• 0
1
vote
2
replies
892
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
20 months ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
816
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 20 months ago by
Marcel Ramos
700 • written 20 months ago by
Astrid Deschênes
• 0
8
votes
5
replies
3.3k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 13 months ago by
Gordon Smyth
53k • written 20 months ago by
Jack S.
▴ 60
4
votes
4
replies
5.2k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 20 months ago by
jandrade
• 0 • written 8.0 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
2
replies
2.0k
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
20 months ago
kcarey
• 0
0
votes
0
replies
706
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
20 months ago
mayra.haedo
• 0
0
votes
0
replies
581
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
20 months ago
erbrocato
• 0
1
vote
4
replies
1.2k
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
20 months ago
samuel.channon
• 0
2
votes
3
replies
844
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 20 months ago by
Michael Love
43k • written 20 months ago by
andrebolerbarros
▴ 20
0
votes
3
replies
950
views
Help with Complex DESeq2 Design
DESeq2
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
kelsey.beavers
• 0
0
votes
1
reply
767
views
Visium RNA
metaMSdata
written 20 months ago by
Karlison
• 0
1
vote
2
replies
1.3k
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
maximilian.beikirch
• 0
0
votes
0
replies
418
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
20 months ago
BID
• 0
0
votes
2
replies
1.1k
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
20 months ago
rocanja
▴ 60
3
votes
3
replies
4.3k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 20 months ago by
snijesh
▴ 200 • written 8.2 years ago by
Ramiro Magno
▴ 100
0
votes
2
replies
3.5k
views
Error in msaFun Cannot open input file. No alignment!
msa
written 20 months ago by
Kamil Slowikowski
▴ 30
2
votes
3
replies
1.1k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
JKim
• 0
0
votes
1
reply
731
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 20 months ago by
Guido Hooiveld
★ 4.1k • written 20 months ago by
Julie
• 0
4
votes
3
replies
1.3k
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 20 months ago by
Georg
• 0
2
votes
2
replies
1.8k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
20 months ago
Eva
▴ 10
46,691 results • Page
28 of 934
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Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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