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0
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1.3k
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Gene co-expression network analysis with small sample size
Network
3.3 years ago
Senthil
• 0
1
vote
2
replies
1.6k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2
scRNAseq
Fluidigm
3.3 years ago • updated 3.2 years ago
evocanres
• 0
0
votes
0
replies
1.2k
views
Edit alignment in msa
alig
msa
Alignment
3.3 years ago
Luis
• 0
0
votes
1
reply
4.0k
views
GEOquery not responding, Error in open.connection(x, "rb") : schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) -…
SEC_E_ILLEGAL_MESSAGE(0x80090326)
handshakefailed
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
moiz_aftab
• 0
0
votes
10
replies
2.7k
views
Peak annotation
HELP
ChIC.data
PeakDetection
ChipOnChipData
3.3 years ago
michela
▴ 20
0
votes
1
reply
1.2k
views
' Update all/some/none? [a/s/n]: '
forensic
expt
updated 3.3 years ago by
tomhenry099
• 0 • written 3.3 years ago by
attia
• 0
0
votes
0
replies
882
views
News:
Bioconductor Code of Conduct Committee Elections 2022
conduct
3.3 years ago
Laurent Gatto
1.6k
2
votes
4
replies
4.0k
views
Normalizing Cut&Tag peak data
Normalization
Peakdata
DiffBind
Cut&Tag
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
bhandary.8590
▴ 20
3
votes
10
replies
3.2k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2
BatchEffect
fold
3.3 years ago • updated 3.2 years ago
eve.olszanowski
• 0
3
votes
6
replies
2.1k
views
Caching bam index files using BiocFileCache
BiocFileCache
3.6 years ago • updated 3.3 years ago
kent.riemondy
▴ 20
0
votes
7
replies
2.2k
views
Help with differential gene expression using Agilent Microarray data (from GEO database)
limma
Paireddata
DifferentialExpression
updated 3.2 years ago by
James W. MacDonald
68k • written 3.3 years ago by
r02eb20
• 0
2
votes
1
reply
1.9k
views
Correcting for all the comparisons that have been made in analysis
DESeq2
comparisons
correction
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
smac_head
• 0
0
votes
0
replies
1.2k
views
News:
New Package Submission Deadline Tomorrow for Bioconductor 3.16
Release
Devel
Bioconductor
Software
3.3 years ago
shepherl
4.3k
1
vote
3
replies
1.9k
views
I can't upgrade to version 3.15 in R
Install
updated 3.3 years ago by
Gordon Smyth
53k • written 3.3 years ago by
dsrlij
• 0
3
votes
4
replies
1.9k
views
I have problems installing DESeq2 using R4.1.2. It tells me that it is not available for my version of R and I need to upgrade my R version. but I ca…
DESeq2
3.3 years ago
yari.hadi
• 0
0
votes
3
replies
1.8k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
3.3 years ago
Madiha
• 0
1
vote
2
replies
1.3k
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2
BatchEffect
3.3 years ago
annamariabugaj
▴ 10
0
votes
3
replies
2.9k
views
Unable to load data "pasillaGenes" in R because DESeq is not installed?
DESeq2
pasillaGenes
updated 3.3 years ago by
James W. MacDonald
68k • written 5.1 years ago by
kanhasunny
• 0
2
votes
1
reply
2.9k
views
Removing metadata rows containing NA values in GRanges
IRanges
GRanges
NA
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
Timucin
• 0
2
votes
2
replies
4.4k
views
Properly constructing a hypergeometric test
overrepresentation
overlap
R
hypergeometric
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
charles.foster
▴ 180
0
votes
1
reply
1.1k
views
I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db
GOfuncR
GO
GOSim
goProfiles
updated 3.3 years ago by
Basti
▴ 780 • written 3.3 years ago by
yeluo
• 0
0
votes
1
reply
2.0k
views
Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2
RNAseq
bulk
DifferentialExpression
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
Maria
• 0
1
vote
1
reply
1.1k
views
Downloading DESeq package manually
DESeq2
Install
updated 3.3 years ago by
Basti
▴ 780 • written 3.3 years ago by
JAcky
• 0
0
votes
0
replies
703
views
GenVisR - adding on genomic positions to CovGen graph
GenVisR
GenCov
3.3 years ago
Amy_
• 0
0
votes
0
replies
875
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO
GeneOntology
LocusIDtogeneIDconversion
3.3 years ago
BioinFo.X
• 0
4
votes
15
replies
6.7k
views
All genes in a set for gseGO funtion
gseGO
setSize
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
Adelyn
▴ 10
3
votes
5
replies
2.4k
views
Biostrings multiple pattern match
pattern
Biostrings
updated 3.3 years ago by
Hervé Pagès
16k • written 3.3 years ago by
fortytwo.teacups
• 0
1
vote
11
replies
7.5k
views
how to merge SummarizedExperiment datasets
summarizedexperiment
updated 3.3 years ago by
spyrouglykeria
• 0 • written 6.3 years ago by
annkolman78
• 0
1
vote
1
reply
3.4k
views
Enhanced Volcano Error when drawing connectors
EnhancedVolcano
updated 3.3 years ago by
Kevin Blighe
★ 4.0k • written 3.3 years ago by
deena.maurer
• 0
0
votes
0
replies
556
views
H bond prediction of two sequences
GeneMeta
generegulation
3.3 years ago
Marcus
• 0
0
votes
0
replies
986
views
Gene Id duplicated
SingleCell
SingleCellData
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
Romina
• 0
1
vote
3
replies
9.2k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome
DESeq2
updated 3.3 years ago by
adR
▴ 40 • written 5.2 years ago by
Daniel
• 0
2
votes
2
replies
3.4k
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
3.3 years ago
Mog
• 0
1
vote
2
replies
3.1k
views
bitr returning unexpected length of gene IDs after conversion.
clusterProfiler
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
quoc.t.nguyen96
• 0
0
votes
1
reply
869
views
Extracting multi-design adjusted counts on DESeq2
DESeq2
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
s26sw
• 0
0
votes
1
reply
1.2k
views
DIfferentially abundant taxa but some of them are not present in both groups (DESeq2)
DESeq2
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
Valentín
• 0
0
votes
1
reply
994
views
DESEQ2 time series with multiple variables
DESeq2
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
Abel
• 0
0
votes
1
reply
1.1k
views
Time serious analysis Wald test in results()
DESeq2
TimeSeriesExperiment
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
Jason
• 0
0
votes
4
replies
1.9k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
3.3 years ago
dario.beraldi
• 0
0
votes
1
reply
1.0k
views
cfDNA pro
cfDNAPro
updated 3.3 years ago by
hw538
• 0 • written 3.3 years ago by
bony.dekumar
▴ 10
1
vote
2
replies
1.8k
views
Limma adj.p.value the same for many different p.values
limmaGUI
limma
adj.p.value
StatisticalMethod
3.3 years ago
walkerrh95
• 0
1
vote
3
replies
1.4k
views
Issue carrying out DiffBind Analysis at a predefined peak set
DiffBind
updated 3.3 years ago by
Rory Stark
★ 5.2k • written 3.3 years ago by
doherta6
• 0
0
votes
1
reply
1.5k
views
Issue with installation of a package.
RStudio
flowFDA
updated 3.3 years ago by
Basti
▴ 780 • written 3.3 years ago by
kinoshamoodley
• 0
0
votes
1
reply
1.0k
views
Champ.impute - myLoad not found
ChAMP
updated 3.3 years ago by
Basti
▴ 780 • written 3.3 years ago by
JD
• 0
3
votes
4
replies
3.1k
views
Comparing different method for DESEQ2
DESeq2
GeneExpression
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
Vapin
• 0
0
votes
6
replies
3.0k
views
No differentially expressed genes after DESeq
DESeq2
R
3.3 years ago
Zach
• 0
9
votes
5
replies
2.5k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10.
karyoploteR
BSgenome
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
rtt100
• 0
0
votes
4
replies
2.3k
views
Questions about non-model organisms gene enrichment analysis
non-model
enrichment
organisms
analysis
updated 3.1 years ago by
Guido Hooiveld
★ 4.1k • written 3.3 years ago by
yuhang
• 0
1
vote
8
replies
2.2k
views
Non-model organism , CluserProfiler message "No gene can be mapped"
organism
non-model
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
yuhang
• 0
0
votes
0
replies
1.4k
views
News:
Bioconductor 3.16 db0s, OrgDbs and TxDbs now available
release
db0
annotation
3.3 years ago
kayla.interdonato
▴ 160
46,712 results • Page
75 of 935
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Comment: Incosistencies in buildSNNGraph() function
by
ATpoint
★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function
by
Aaron Lun
★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops!
by
TikTsokaas33ocissalpc
• 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Votes
Answer: Incosistencies in buildSNNGraph() function
Answer: Where do the filename come from in the LOLA datasets?
Bioconductor Maintainer Application
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
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