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1
vote
0
replies
671
views
Attempting to import SBML file using R
SBMLR
sbml
rsbm
rsbml
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
isasg
▴ 10
0
votes
0
replies
1.0k
views
help with converting MSTRG tags with isoformswictanalyzer
stringtie
IsoformSwitchAnalyzeR
pfamAnalyzeR
gtf
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
sumitra.20
• 0
0
votes
0
replies
731
views
Cannot read biom file in R
RESOLVE
updated 2.1 years ago by
shepherl
4.2k • written 2.1 years ago by
Jashvant Kumar
• 0
1
vote
1
reply
637
views
Minimum datasets needed for meta analysis
RnaSeqSampleSize
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Durga
▴ 10
0
votes
0
replies
642
views
Normalising processed Proteomics data in R
Bioconductor
Proteomics
2.1 years ago
Joshua
• 0
0
votes
1
reply
926
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Ana
• 0
0
votes
0
replies
832
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
2.1 years ago
vasily.dobrovolsky
• 0
0
votes
1
reply
795
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 2.1 years ago by
Gordon Smyth
53k • written 2.1 years ago by
glopez
• 0
0
votes
0
replies
619
views
GaussNorm fails to recognize flowFrames in flowSet as individual elements
flowStats
2.1 years ago
mikkel.byrdal
• 0
0
votes
0
replies
1.0k
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
2.1 years ago
jared.andrews07
▴ 30
0
votes
0
replies
632
views
accesing gene name RNAseq
genetics
GeneticsPed
Genetics
2.1 years ago
Gülsüm
• 0
0
votes
0
replies
731
views
Identifying populations within a FlowSOM tree
FlowSOM
2.1 years ago
agus_rizzo
• 0
0
votes
1
reply
686
views
COTAN mantainance
BuildReport
updated 2.1 years ago by
shepherl
4.2k • written 2.1 years ago by
Silvia
• 0
0
votes
0
replies
1.6k
views
Version map cannot be validated - not mapping to new bioconductor website
Install
2.1 years ago
Alexander
• 0
0
votes
0
replies
501
views
R/sql code to find the haplotype data from patient's rsIDs
starallele
phenoTest
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
greeshmathulasi1
• 0
0
votes
1
reply
651
views
Incorrect display of Y-axis
trackViewer
updated 2.1 years ago by
Ou, Jianhong
★ 1.3k • written 2.1 years ago by
Bastien
• 0
0
votes
2
replies
924
views
combat output NaN
sva
2.1 years ago
maxixian1990
• 0
0
votes
1
reply
910
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData
DESeq2
updated 2.1 years ago by
Wolfgang Huber
★ 13k • written 2.1 years ago by
meroy
• 0
0
votes
2
replies
936
views
Cannot open Sysmex Partec CUbe 6 .fcs with read.FCS
Partec
read.FCS
flowCore
2.1 years ago
mrescan
• 0
0
votes
0
replies
608
views
nondetects and technical replicates
qPCR
nondetects
2.1 years ago
Ed Siefker
▴ 230
0
votes
0
replies
614
views
SGSeq how export PSI values for each typr of splice variant
SGSeq
2.1 years ago
Alison
• 0
0
votes
3
replies
1.4k
views
Support for installation and usage of TxDb.Hsapiens.UCSC.hg19.knownGene package in R version 4.2.2
Bioconductor
BiocPkgTools
2.1 years ago
blessybo
• 0
0
votes
0
replies
877
views
Gviz::GeneRegionTrack error with standard TxDb: "adding seqlevels to a TxDb object is not supported"
Gviz
2.1 years ago
dbsgtk
• 0
1
vote
0
replies
1.1k
views
Gviz : UcscTrack
rtracklayer
UCSC
Gviz
2.1 years ago
yujin
▴ 10
1
vote
1
reply
959
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
2.2 years ago
NiKo
▴ 10
0
votes
0
replies
748
views
Mfuzz package loading issues
Mfuzz
MacBook
loadingissues
2.2 years ago
Jon
• 0
0
votes
1
reply
676
views
Advice needed on package using online databases (fails CHECK when database is down)
Bioconductor
updated 2.2 years ago by
shepherl
4.2k • written 2.2 years ago by
Marek Gierlinski
▴ 30
0
votes
0
replies
866
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
2.2 years ago
mch
• 0
0
votes
4
replies
1.6k
views
Mfuzz package loading issues
Mfuzz
loadingissues
macbook
2.2 years ago
Jon
• 0
0
votes
2
replies
871
views
Can you help me generate a Bsgenome of the fusion genome of a human and HIV-1 virus?
BSgenome.Hsapiens.NCBI.GRCh38
2.2 years ago
13273976287
• 0
2
votes
10
replies
2.4k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
2.2 years ago • updated 2.1 years ago
rohitsatyam102
▴ 20
0
votes
3
replies
1.2k
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
Marilyn
• 0
0
votes
2
replies
1.0k
views
can't update bioconductor 3.18
BioCor
bioc
BiocVersion
2.2 years ago
feifan
• 0
1
vote
2
replies
1.3k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 2.2 years ago by
meenae
▴ 10
0
votes
0
replies
671
views
proActiv - Error in estimateSizeFactorsForMatrix when using the proActiv function
proActiv
error
estimateSizeFactorsForMatrix
2.2 years ago
Chris
• 0
0
votes
1
reply
1.6k
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
2.2 years ago
leon
• 0
0
votes
0
replies
761
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
2.2 years ago
Sara
• 0
0
votes
2
replies
775
views
DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
2.2 years ago
Roey Angel
• 0
0
votes
4
replies
1.7k
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO
ensembldb
2.2 years ago
Rockbar
• 0
2
votes
0
replies
583
views
bioNeuro plot_expression_profile - how to order samples in plot output
plot_expression_profile
BioNERO
2.2 years ago
Christopher
▴ 20
0
votes
0
replies
749
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
2.2 years ago
Florian
• 0
0
votes
0
replies
1.0k
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
2.2 years ago
Xinqi
• 0
0
votes
0
replies
918
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
2.2 years ago
Sara
• 0
0
votes
0
replies
728
views
How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS
admixMap
2.2 years ago
mailtoshivam13
• 0
0
votes
0
replies
893
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler
DifferentialExpression
2.2 years ago
nromerov
• 0
0
votes
1
reply
1.1k
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.2 years ago by
megan
• 0
0
votes
0
replies
586
views
loadstudy and cBioDataPack return error in vroom_
cBioPortalData
2.2 years ago
karam
• 0
0
votes
0
replies
978
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
sophie.hfliu
• 0
0
votes
1
reply
841
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 20 months ago by
Lluís Revilla Sancho
▴ 760 • written 2.2 years ago by
karmasstark
• 0
0
votes
2
replies
981
views
bug in block.plsda from mixOmics?
mixOmics
2.2 years ago
Lluís Revilla Sancho
▴ 760
1,000 results • Page
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Comment: nice 3D displays for PCA analysis
by
adam80haynes
• 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital
by
TikTsokaasocissalpc
• 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
TikTsokaasocissalpc
• 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long?
by
ATpoint
★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
Votes
Limma-voom sample weights and impact on DEG numbers
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
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