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0
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5
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find tandem repeats in DNA
DNA
repeats
1 hour ago
me-nobody
• 0
8
votes
7
replies
129
views
MA plot
MAplot
updated 32 minutes ago by
Guido Hooiveld
★ 3.5k • written 1 day ago by
Nathalie
• 0
0
votes
3
replies
78
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR
RNAseq
updated 9 hours ago by
Gordon Smyth
47k • written 17 hours ago by
k.roelfs
• 0
1
vote
2
replies
50
views
transcript name mapping between human and mouse
biomaRt
getLDS
22 hours ago • updated 3 hours ago
Eric
• 0
0
votes
1
reply
27
views
I cannot install annotables package in Rstudio (macOS)
DESeq2
PackageTypeData
package
Annotation
updated 18 hours ago by
Mike Smith
★ 5.8k • written 19 hours ago by
m-bihie
• 0
1
vote
3
replies
79
views
How can I draw a barplot of complexheatmap according 'Tumor Type'
heatma
heatmaps
ComplexHeatmap
updated 21 hours ago by
elefth.pavlos
▴ 30 • written 2 days ago by
Sooni
• 0
3
votes
5
replies
103
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 14 hours ago by
Michael Love
39k • written 1 day ago by
aditya.m
▴ 10
0
votes
0
replies
22
views
Rsubread align every slow in mac but faster in windows
Rsubread
1 day ago
Wei
• 0
2
votes
4
replies
76
views
ComplexHeatmap - Default distance and hierarchical clustering methods
ComplexHeatmap
Complex
updated 22 hours ago by
elefth.pavlos
▴ 30 • written 1 day ago by
Katharina
• 0
0
votes
1
reply
41
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 23 hours ago by
ATpoint
★ 2.1k • written 1 day ago by
m-bihie
• 0
0
votes
1
reply
47
views
DESeq2 in R 4.2.2
DESeq2
SummarizedExperiment
DelayedArray
updated 23 hours ago by
ATpoint
★ 2.1k • written 1 day ago by
Danielle
• 0
0
votes
3
replies
71
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb
biodbUniprot
updated 17 hours ago by
James W. MacDonald
62k • written 1 day ago by
Peter
• 0
0
votes
0
replies
26
views
msa module crash
msa
1 day ago
systems
• 0
0
votes
0
replies
46
views
News:
Seeking members for BioC2023 organizing committee
BioC2023
Bioconductor
community
1 day ago • updated 22 hours ago
Maria Doyle
▴ 10
0
votes
1
reply
53
views
about deltaPSI
SpliceWiz
updated 2 days ago by
a.wong
▴ 10 • written 2 days ago by
reza.rahman
• 0
2
votes
2
replies
92
views
Volcano Plot in R
cellxgenedp
updated 2 days ago by
Gordon Smyth
47k • written 2 days ago by
Rashi
▴ 10
0
votes
1
reply
862
views
limma: decideTests
affy
limma
affy
limma
updated 2 days ago by
Gordon Smyth
47k • written 15.1 years ago by
Al Ivens
▴ 270
0
votes
3
replies
102
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
2 days ago • updated 1 day ago
martin.grigorov
• 0
1
vote
0
replies
108
views
News:
Join the Community Advisory Board -- upcoming elections -- deadline January 31st
Bioconductor
CAB
bioconductoroversight
community
6 weeks ago • updated 2 days ago
shepherl
3.4k
0
votes
1
reply
51
views
convert local downloaded bigwig files to .bed files
BRgen
BRGenomics
updated 2 days ago by
ATpoint
★ 2.1k • written 3 days ago by
kavator
▴ 20
0
votes
1
reply
63
views
NAs in some genes in topTable output
limma
topTable
updated 3 days ago by
Gordon Smyth
47k • written 3 days ago by
thkapell
▴ 10
0
votes
1
reply
48
views
limma on spectral data
limma
Metabolomics
DifferentialExpression
POMA
updated 3 days ago by
Gordon Smyth
47k • written 3 days ago by
wiscoyogi
• 0
0
votes
1
reply
83
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 3 days ago by
Michael Love
39k • written 7 days ago by
joanna
• 0
0
votes
1
reply
68
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 3 days ago by
Michael Love
39k • written 3 days ago by
kalavattam
• 0
1
vote
2
replies
68
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
3 days ago • updated 9 hours ago
Bernardo
• 0
0
votes
1
reply
55
views
Subset count data in DGEList using edgeR/DESeq2
edgeR
DMR
updated 3 days ago by
Michael Love
39k • written 3 days ago by
Fiona
• 0
0
votes
2
replies
70
views
scanBam
Rsamtools
Rsam
updated 3 days ago by
Martin Morgan
25k • written 4 days ago by
jojo.valensi
• 0
2
votes
3
replies
94
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db
AnnotationDbi
updated 3 days ago by
James W. MacDonald
62k • written 3 days ago by
harish
• 0
0
votes
0
replies
19
views
INSPEcT: How to get the RNA dynamics for steady-state with INSPEcT minus
INSPEcT
3 days ago
MK
• 0
0
votes
2
replies
85
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 3 days ago by
Rory Stark
★ 4.6k • written 8 days ago by
slrpatty
• 0
2
votes
3
replies
843
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 4 days ago by
stefano.mangiola
▴ 10 • written 4.0 years ago by
ramonmassoni
▴ 10
1
vote
3
replies
96
views
SpliceWiz collateData error
SpliceWiz
written 7 days ago by
chiara.caprioli
• 0
2
votes
2
replies
94
views
[DESeq2] There is no difference in expression in my heatmap
DESeq2
heatmaps
4 days ago • updated 2 days ago
Sooni
• 0
0
votes
0
replies
56
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
4 days ago
S
• 0
0
votes
1
reply
63
views
GRanges list convert into igraph format
GRanges
igraph
updated 2 days ago by
Lluís Revilla Sancho
▴ 700 • written 5 days ago by
Bogdan
▴ 660
0
votes
1
reply
77
views
Extracting interaction contrast when using user supplied model.matrix
DESeq2
updated 5 days ago by
Michael Love
39k • written 6 days ago by
idetoma
• 0
0
votes
3
replies
129
views
Genes for a given chromosome
GRangesobjectmodification
updated 3 days ago by
James W. MacDonald
62k • written 6 days ago by
Gamal
• 0
0
votes
0
replies
30
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
6 days ago
Delta._.43
▴ 20
0
votes
0
replies
27
views
News:
Seeking Outreachy interns and project proposals
Bioconductor
Outreachy
community
6 days ago
Maria Doyle
▴ 10
0
votes
0
replies
54
views
Installation had non-zero exit status for all Bioconductor packages
Bioconductor
6 days ago
Anastasia
• 0
1
vote
3
replies
174
views
DESeq2 Installation Issue
DESeq2
updated 7 days ago by
Hervé Pagès
16k • written 7 days ago by
joanna
• 0
0
votes
1
reply
53
views
MSc student
genomes
updated 6 days ago by
Basti
▴ 530 • written 7 days ago by
Deeplaxmi
• 0
0
votes
1
reply
76
views
RUV with K more than 1.
RUVSeq
updated 7 days ago by
ATpoint
★ 2.1k • written 7 days ago by
star
▴ 10
2
votes
4
replies
129
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2
DifferentialExpression
updated 3 days ago by
Michael Love
39k • written 7 days ago by
idetoma
• 0
0
votes
1
reply
71
views
Rnaseq analysis using a continuous time series
DESeq2
updated 7 days ago by
Michael Love
39k • written 8 days ago by
Aviads
• 0
0
votes
2
replies
82
views
installing DESeq2 on Macbook R Studio
DESeq2
updated 7 days ago by
Michael Love
39k • written 8 days ago by
Chatura
• 0
0
votes
1
reply
54
views
More information on results columns
DESeq2
updated 7 days ago by
ATpoint
★ 2.1k • written 7 days ago by
krigerkoalaen
• 0
0
votes
2
replies
95
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 8 days ago by
Gordon Smyth
47k • written 8 days ago by
Keith
• 0
3
votes
4
replies
127
views
Processing data with voom "expression values" and "weights"
limma
voom
updated 7 days ago by
Gordon Smyth
47k • written 8 days ago by
Edmond
• 0
1
vote
1
reply
53
views
how to call an app from Cytoscape using R?
RCy3
updated 8 days ago by
alex.pico
• 0 • written 8 days ago by
adR
▴ 20
43,697 results • Page
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Comment: MA plot
by
Guido Hooiveld
★ 3.5k
Yes, some of the values in your input don't make sense. Yet, since you just started learning below some code to use to read in a tab delim…
Comment: transcript name mapping between human and mouse
by
Eric
• 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Bernardo
• 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report
by
Okan
• 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Votes
Comment: Combat and dds Object
Answer: How can I draw a barplot of complexheatmap according 'Tumor Type'
Comment: MA plot
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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