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Views
Votes
0
votes
0
replies
80
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping
AnnotationHub
multiGSEA
9 days ago
Thomas
• 0
0
votes
5
replies
113
views
Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2
longitudinal
updated 6 days ago by
swbarnes2
★ 1.2k • written 9 days ago by
sharvari gujja
▴ 40
3
votes
2
replies
92
views
Help with the design matrix for longitudinal study
edgeR
9 days ago
sharvari gujja
▴ 40
1
vote
9
replies
200
views
Is it possible to annotate a GRanges Object that has scaffolding names and not chromosome numbers?
Annotation
updated 3 days ago by
James W. MacDonald
62k • written 9 days ago by
stacy.genovese
• 0
4
votes
4
replies
133
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 8 days ago by
James W. MacDonald
62k • written 10 days ago by
Dario Strbenac
★ 1.5k
2
votes
4
replies
108
views
Successor of genesBy Defunct Function
ensembldb
updated 8 days ago by
Hervé Pagès
16k • written 10 days ago by
Dario Strbenac
★ 1.5k
1
vote
2
replies
96
views
select with org.Mm.eg.db does not give ENSEMBL ids
org.Mm.eg.db
10 days ago • updated 9 days ago
raf4
▴ 20
4
votes
7
replies
187
views
DESeq2: Repetitive padj values?
DESeq2
updated 3 days ago by
Michael Love
39k • written 10 days ago by
vanbelj
▴ 20
0
votes
1
reply
104
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 9 days ago by
Dario Strbenac
★ 1.5k • written 11 days ago by
Hicham
• 0
0
votes
1
reply
119
views
Is this DESeq2 interactions design correct?
DESeq2
interactions
updated 12 days ago by
Michael Love
39k • written 13 days ago by
bhagyesh
• 0
0
votes
8
replies
258
views
DropletUtils::read10xCounts error
read10xCounts
DropletUtils
13 days ago • updated 10 days ago
fdumetz
• 0
0
votes
3
replies
167
views
how to iterate all comparisons in group with "coef =" ?
DESeq2
updated 3 days ago by
Michael Love
39k • written 13 days ago by
theodore.georgomanolis
• 0
0
votes
3
replies
150
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures
R
genomation
bed
updated 9 days ago by
James W. MacDonald
62k • written 13 days ago by
sat
• 0
0
votes
2
replies
123
views
Online Venn diagram generator where I can paste text files containing gene name lists to get the diagram
Venndiagram
files
text
14 days ago
ratto
• 0
0
votes
1
reply
78
views
How to set threshold of padj value in DeSeq2
DESeq2
padj
default
updated 14 days ago by
James W. MacDonald
62k • written 14 days ago by
Serena
• 0
0
votes
3
replies
78
views
GSVA results interpretation
GSVA
updated 13 days ago by
Robert Castelo
★ 3.0k • written 14 days ago by
munta.jihad
• 0
0
votes
1
reply
70
views
Combining VST counts for replicates
DESeq2
updated 14 days ago by
Michael Love
39k • written 15 days ago by
Jayesh Kumar
• 0
3
votes
3
replies
143
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 15 days ago by
Gordon Smyth
47k • written 15 days ago by
Sara
• 0
0
votes
1
reply
66
views
Differential RNA seq on TCGA set
DESeq2
RNASeqData
updated 15 days ago by
ATpoint
★ 2.0k • written 15 days ago by
SilverCat
• 0
0
votes
3
replies
103
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb
AnnotationDbi
AnnotationForge
updated 7 days ago by
James W. MacDonald
62k • written 15 days ago by
ahiser
• 0
0
votes
2
replies
111
views
Orange point meaning in plotSmear with edgeR
edgeR
plotSmear
15 days ago • updated 14 days ago
Tess
• 0
0
votes
0
replies
63
views
adding peptides to a multiple sequence alignment
msa
IRanges
Biostrings
15 days ago
Mario Dejung
• 0
0
votes
1
reply
53
views
rlog() transformation works only when using DESeqDataSet, not matrix
DESeq2
updated 15 days ago by
Michael Love
39k • written 15 days ago by
licheny
• 0
1
vote
0
replies
73
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn
vsn
Normalization
vsn2
Proteomics
15 days ago • updated 13 days ago
Arend
▴ 10
0
votes
1
reply
63
views
Help needed to run PVCA
pvca
updated 15 days ago by
James W. MacDonald
62k • written 15 days ago by
jyotsna.rao
• 0
0
votes
1
reply
51
views
Error in ATACseqQC bamQC analysis
ATACSeq
ATACseqQC
updated 15 days ago by
Ou, Jianhong
★ 1.3k • written 16 days ago by
tahir.msajid
• 0
0
votes
0
replies
37
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
16 days ago
cathalgking
• 0
0
votes
2
replies
108
views
Time series between two conditions with a common time zero
timeseries
updated 15 days ago by
James W. MacDonald
62k • written 16 days ago by
Brynn
• 0
0
votes
2
replies
89
views
Differential expression between samples of the same group
DESeq2
16 days ago • updated 10 days ago
Oded
• 0
0
votes
0
replies
51
views
Job:
PhD position in Bioinformatics in Jena
Statistics
ComputationalBiology
Aging
MachineLearning
16 days ago
alena.vanboemmel
• 0
2
votes
2
replies
114
views
Estimating Fold-Changes of Lowly Expressed Genes
limma
17 days ago • updated 16 days ago
vm
▴ 30
0
votes
1
reply
119
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 14 days ago by
Michael Love
39k • written 17 days ago by
Jayesh Kumar
• 0
2
votes
1
reply
86
views
Read zipped H5AD file directly
rhdf5
updated 16 days ago by
Mike Smith
★ 5.8k • written 17 days ago by
merv
▴ 60
0
votes
2
replies
86
views
EpiDISH- from Genomic Cordinate
genomic
EpiDISH
updated 16 days ago by
shijieczheng
• 0 • written 17 days ago by
bony.dekumar
• 0
0
votes
2
replies
92
views
microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene
microRNA
TxDb.Hsapiens.UCSC.hg38.knownGene
17 days ago • updated 14 days ago
Lluís Revilla Sancho
▴ 700
0
votes
2
replies
107
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 17 days ago by
camilia.savitri
• 0
0
votes
2
replies
124
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
18 days ago • updated 17 days ago
dqt
• 0
0
votes
3
replies
130
views
Add GP values to VCF
VariantAnnotation
19 days ago • updated 13 days ago
Stephanie M. Gogarten
▴ 820
2
votes
2
replies
139
views
Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
19 days ago • updated 9 days ago
SciencyUsagi
▴ 10
0
votes
1
reply
99
views
Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression
limma
R
TissueMicroarrayData
updated 19 days ago by
Gordon Smyth
47k • written 19 days ago by
Элина
• 0
0
votes
1
reply
161
views
Help for RNA sequencing analysis with DESEQ2
DESeq2
star
differentiallyexpressed
updated 14 days ago by
Michael Love
39k • written 20 days ago by
nico
• 0
0
votes
0
replies
50
views
KEGGREST API keggLink and keggGet for hsa:5164
reactions
hsa:5164
20 days ago
susrinivasan
• 0
0
votes
8
replies
237
views
Question about Diffbind counts
DiffBind
20 days ago • updated 7 days ago
slrpatty
• 0
0
votes
1
reply
91
views
Missing transcript
DESeq2
tximport
salmon
updated 20 days ago by
ATpoint
★ 2.0k • written 20 days ago by
camilia.savitri
• 0
1
vote
3
replies
176
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
21 days ago • updated 20 days ago
Alexandre
• 0
0
votes
1
reply
75
views
dba.count Error in DiffBind
DiffBind
21 days ago
narzouni
• 0
1
vote
4
replies
122
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
21 days ago
Iwan
• 0
1
vote
3
replies
164
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2
edgeR
rnaseqGene
updated 14 days ago by
Michael Love
39k • written 22 days ago by
vpl685
• 0
0
votes
3
replies
135
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2
edgeR
22 days ago • updated 21 days ago
ubjw24
• 0
1
vote
4
replies
127
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq
PeakDetection
22 days ago • updated 9 days ago
stacy.genovese
• 0
43,696 results • Page
2 of 874
Recent ...
Replies
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…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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