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1
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2
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1.3k
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Problems with Feature counting
Rsubread
BAMfiles
GTFfile
2.0 years ago
mirjanakessler
• 0
0
votes
0
replies
1.0k
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
2.0 years ago
Jawahar
• 0
2
votes
4
replies
2.8k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
2.0 years ago
Sabiha
▴ 20
0
votes
2
replies
895
views
Which fasta files to use for tximeta makeLinkTxome
tximeta
DESeq2
2.0 years ago
JING
• 0
5
votes
6
replies
1.6k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
2.0 years ago
Shaimaa Gamal
• 0
0
votes
1
reply
556
views
DESEQ2 reduced model input into Pathfindr
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
a.raftery.1
• 0
0
votes
1
reply
826
views
Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2
timecourse
time
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
Anastasiia
• 0
2
votes
2
replies
1.1k
views
Deleting a column from data frame and then running DESeq2
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
amv112
▴ 10
0
votes
2
replies
2.1k
views
Plotting mean TPM of an expressed gene
DESeq2
2.0 years ago • updated 24 months ago
mp52226
• 0
0
votes
1
reply
933
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
manuel
• 0
4
votes
6
replies
1.7k
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
2.0 years ago
Dario Strbenac
★ 1.6k
0
votes
3
replies
1.4k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
annasoudi
• 0
0
votes
0
replies
560
views
How to search for a string in a DNAStringSet dataset?
Biostrings
2.0 years ago
Angela Michalichyn
• 0
0
votes
0
replies
567
views
rpk per cell saved in SCE object.
SingleCellExperiment
2.0 years ago
JalapenoCornbread
• 0
0
votes
0
replies
655
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
2.0 years ago
frueher
• 0
3
votes
3
replies
2.1k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
Jurgen
• 0
2
votes
17
replies
4.7k
views
Problem installing package, version of dependency issue
AnnotationDbi
GO.db
updated 2.0 years ago by
Lluís Revilla Sancho
▴ 760 • written 2.0 years ago by
alexandre.blais
▴ 50
0
votes
1
reply
647
views
[DESEQ2] When to average biological replicates for hierarchical clustering
DESeq2
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
E
• 0
2
votes
2
replies
647
views
How to interpret log2fold values when using numeric contrasts in DESEQ2?
DESeq2
2.0 years ago
pl23
• 0
1
vote
1
reply
2.3k
views
Error with biomaRt
biomaRt
updated 2.0 years ago by
Mike Smith
★ 6.6k • written 2.0 years ago by
goldenboy
• 0
2
votes
2
replies
815
views
How to contact Bioconductor's test host?
Bioconductor
updated 2.0 years ago by
Hervé Pagès
16k • written 2.0 years ago by
Marek Gierlinski
▴ 30
4
votes
2
replies
1.4k
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 2.0 years ago by
Guido Hooiveld
★ 4.1k • written 2.0 years ago by
sansan
• 0
1
vote
3
replies
924
views
makeOrgPackageFromNCBI generates an empty database?
OrganismDbi
makeOrgPackageFromNCBI
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
dissikratzl
• 0
2
votes
2
replies
1.7k
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
2.0 years ago
bd2000
▴ 30
0
votes
4
replies
3.0k
views
Bioconductor installation
Bioconductor
written 2.1 years ago by
Akhil
• 0
0
votes
3
replies
1.6k
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel
scran
updated 2.0 years ago by
ATpoint
★ 5.0k • written 2.0 years ago by
qwang178
• 0
0
votes
3
replies
1.5k
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet
GInteractions
2.0 years ago
Sarah
▴ 10
4
votes
6
replies
1.8k
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 23 months ago by
Gordon Smyth
53k • written 2.0 years ago by
Shaimaa Gamal
• 0
0
votes
0
replies
589
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
2.0 years ago
Vincent J. Carey, Jr.
6.7k
3
votes
1
reply
956
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
Shaimaa Gamal
• 0
0
votes
0
replies
586
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
2.0 years ago
Aswathy
• 0
1
vote
1
reply
763
views
Looking for a MSigDB chip file
DESeq2
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
Katherine
• 0
0
votes
1
reply
1.1k
views
DESeq2 multi-factor design and interaction terms
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
KW
• 0
0
votes
3
replies
1.7k
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 2.0 years ago by
Fayrouz
• 0
2
votes
5
replies
1.6k
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
2.0 years ago
ctlong
• 0
2
votes
7
replies
1.4k
views
distanceToNearest
rtracklayer
ranges
distanceToNearest
2.0 years ago
robjohn70000
• 0
1
vote
0
replies
842
views
News:
Ensembl 111 has been released
Ensembl
biomaRt
2.0 years ago
Benjamin
▴ 30
0
votes
1
reply
703
views
Conversion of .sf to .rgel format for the salmon processed files with transcript to gene mapping.
RnaSeqSampleSize
updated 2.0 years ago by
ATpoint
★ 5.0k • written 2.0 years ago by
Anudev
• 0
0
votes
0
replies
863
views
News:
Online course - Flow cytometry data analysis with R/Bioconductor
flowDensity
flowCore
2.0 years ago
info
▴ 10
4
votes
5
replies
1.7k
views
Bioconductor code browser time out
Bioconductor
updated 7 months ago by
Mike Smith
★ 6.6k • written 2.0 years ago by
Marek Gierlinski
▴ 30
4
votes
9
replies
2.6k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
2.1 years ago • updated 2.0 years ago
Luca
• 0
1
vote
2
replies
1.2k
views
Access genes associated with GO terms for a topGO object created with gene2GO
topGO
2.0 years ago
Dan
• 0
0
votes
0
replies
578
views
annotatr rn7?
annotatr
2.1 years ago
chuanjiao6
• 0
0
votes
1
reply
881
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
2.1 years ago
WS
• 0
0
votes
3
replies
2.9k
views
DESeq2 design with multiple factors
DESeq2
written 2.1 years ago by
KW
• 0
0
votes
1
reply
1.1k
views
Mismatch between MAST DE results and expression dot plot
MAST
mastR
2.1 years ago
Simon
• 0
0
votes
0
replies
1.0k
views
Job:
Openings for Doctoral Researchers at the University of Helsinki
easyreporting
MolecularMedicine
LifeSciences
bioinformatics
2.1 years ago
rubina.tabassum
• 0
1
vote
1
reply
1.1k
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
phmai1148
• 0
0
votes
1
reply
643
views
download problem
edgeR
updated 2.1 years ago by
Gordon Smyth
53k • written 2.1 years ago by
theokirkland3
• 0
1
vote
3
replies
1.3k
views
Read Count Normalisation and validation of analysis
DifferentialExpression
DESeq2
written 2.1 years ago by
Dinesh
• 0
46,734 results • Page
35 of 935
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Replies
Answer: Confirm that OpenStats will not be archived (pryr dependency)
by
shepherl
4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Michael Love
43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Federico Marini
▴ 180
Jumping in on this - all this started because we want to "do it right", i.e. avoiding the post-hoc filtering on the logFC (which is still w…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Michael Love
43k
it looks above like you have a gene with two non-zero count samples. Also, yes you can use a stricter filter. You cannot estimate the LFC …
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Ahmed Salah
• 0
Thank you very much for your answer. Actually, this is after pre-filtering ```r keep <- rowSums(counts(dds) >= 10) >= 3 dds <- dds[keep, …
Votes
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
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