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7
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Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
27 days ago • updated 25 days ago
needNGS
• 0
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
28 days ago • updated 7 days ago
Chris
• 0
3
votes
5
replies
349
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 27 days ago by
Gordon Smyth
50k • written 29 days ago by
Fabian
• 0
0
votes
2
replies
167
views
Minfi - estimatecellscount
min
minfi
28 days ago
clacarion
• 0
0
votes
0
replies
100
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
29 days ago
feather-W
• 0
0
votes
0
replies
100
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
29 days ago
Ankit
▴ 20
0
votes
6
replies
324
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 28 days ago by
Gordon Smyth
50k • written 29 days ago by
Faisal
• 0
1
vote
5
replies
308
views
fgsea fork
fgsea
updated 28 days ago by
James W. MacDonald
65k • written 29 days ago by
yimjohns
• 0
0
votes
1
reply
146
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 29 days ago by
Michael Love
41k • written 29 days ago by
Mikushi
• 0
0
votes
0
replies
86
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
4 weeks ago
Pierre Lindenbaum
▴ 10
2
votes
8
replies
504
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
Amit
• 0
0
votes
1
reply
124
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Karen
• 0
2
votes
3
replies
335
views
PCA of different bacterial species
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Laura
▴ 10
1
vote
2
replies
224
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
4 weeks ago
Mj.A.
• 0
0
votes
1
reply
245
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
7 weeks ago • updated 4 weeks ago
shepherl
3.8k
0
votes
2
replies
197
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
SG
• 0
2
votes
3
replies
244
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 4 weeks ago by
Wei Shi
★ 3.6k • written 4 weeks ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
208
views
From a DNAStringSet to a data.frame
Biostrings
4 weeks ago
ramiro.barrantes
▴ 10
0
votes
1
reply
163
views
collapseReplicates dimension error
DESeq2
Dese
updated 4 weeks ago by
Michael Love
41k • written 5 weeks ago by
Léa
• 0
5
votes
25
replies
832
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 22 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Jitendra
▴ 10
0
votes
2
replies
167
views
bioconductor emailing list
Bioconductor
updated 4 weeks ago by
shepherl
3.8k • written 4 weeks ago by
1427972815
• 0
3
votes
2
replies
203
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
4 weeks ago
Anita
▴ 10
3
votes
3
replies
373
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 4 weeks ago by
alan.ocallaghan
▴ 160 • written 4 weeks ago by
Najla Abassi
• 0
2
votes
1
reply
227
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 4 weeks ago by
ATpoint
★ 4.0k • written 4 weeks ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
109
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
4 weeks ago
gshweta95
• 0
0
votes
2
replies
333
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 24 days ago
Gordon
• 0
7
votes
6
replies
436
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
2
votes
1
reply
196
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 4 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
enee
▴ 10
0
votes
0
replies
132
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
5 weeks ago
Maria Doyle
▴ 70
0
votes
0
replies
119
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
5 weeks ago
shepherl
3.8k
0
votes
1
reply
220
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
scoops_streams_06
• 0
0
votes
0
replies
110
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
5 weeks ago
nromerov
• 0
1
vote
2
replies
221
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
5 weeks ago • updated 4 weeks ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
249
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 5 weeks ago by
Marcel Ramos
690 • written 5 weeks ago by
Astrid Deschênes
• 0
5
votes
3
replies
695
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Jack S.
▴ 50
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 5 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
2
replies
214
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
5 weeks ago
kcarey
• 0
0
votes
0
replies
119
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
5 weeks ago
mayra.haedo
• 0
0
votes
0
replies
108
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
5 weeks ago
taylor.witte
• 0
0
votes
0
replies
127
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
5 weeks ago
erbrocato
• 0
1
vote
4
replies
276
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
5 weeks ago
samuel.channon
• 0
2
votes
3
replies
288
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
andrebolerbarros
▴ 20
0
votes
3
replies
248
views
Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
kelsey.beavers
• 0
0
votes
2
replies
193
views
Visium RNA
metaMSdata
updated 5 weeks ago by
vvvc360work2
• 0 • written 5 weeks ago by
Karlison
• 0
1
vote
2
replies
268
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
111
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
5 weeks ago
BID
• 0
1
vote
3
replies
259
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 4 weeks ago by
mercedeh.movassagh
▴ 10 • written 5 weeks ago by
María
• 0
0
votes
2
replies
200
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
5 weeks ago
rocanja
▴ 60
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 5 weeks ago by
snijesh
▴ 20 • written 6.6 years ago by
Ramiro Magno
▴ 100
0
votes
2
replies
217
views
Error in msaFun Cannot open input file. No alignment!
msa
written 5 weeks ago by
Kamil Slowikowski
▴ 30
45,581 results • Page
4 of 912
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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