4
votes
4
replies
133
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 8 days ago by 62k • written 10 days ago by ★ 1.5k
0
votes
3
replies
97
views
Do the count values should be only integer to be able to use DESeq2?
DESeq2
8 days ago Sepehr • 0
0
votes
1
reply
45
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Updated package is not the version specified on the homepage
Versions Update BindingSiteFinder
updated 8 days ago by ★ 5.8k • written 8 days ago by • 0
0
votes
5
replies
113
views
Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2 longitudinal
updated 6 days ago by ★ 1.2k • written 9 days ago by ▴ 40
1
vote
3
replies
102
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Adding ellipse in PCAtools biplot
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updated 8 days ago by 3.7k • written 9 days ago by • 0
0
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0
replies
80
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multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
9 days ago Thomas • 0
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
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Is it possible to annotate a GRanges Object that has scaffolding names and not chromosome numbers?
Annotation
updated 3 days ago by 62k • written 9 days ago by • 0
2
votes
4
replies
108
views
Successor of genesBy Defunct Function
ensembldb
updated 8 days ago by 16k • written 10 days ago by ★ 1.5k
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 ★ 1.5k • written 11 days ago by • 0
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
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DESeq2: Repetitive padj values?
DESeq2
updated 3 days ago by 39k • written 10 days ago by ▴ 20
0
votes
1
reply
119
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 12 days ago by 39k • written 13 days ago by • 0
0
votes
3
replies
167
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how to iterate all comparisons in group with "coef =" ?
DESeq2
updated 3 days ago by 39k • written 13 days ago by • 0
0
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8
replies
258
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DropletUtils::read10xCounts error
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13 days ago • updated 10 days ago fdumetz • 0
0
votes
3
replies
150
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Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 9 days ago by 62k • written 13 days ago by • 0
0
votes
2
replies
107
views
how to match salmon output to txname
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written 17 days ago by • 0
0
votes
2
replies
123
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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
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
119
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 14 days ago by 39k • written 17 days ago by • 0
0
votes
1
reply
161
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Help for RNA sequencing analysis with DESEQ2
DESeq2 star differentiallyexpressed
updated 14 days ago by 39k • written 20 days ago by • 0
1
vote
3
replies
164
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 14 days ago by 39k • written 22 days ago by • 0
0
votes
1
reply
70
views
Combining VST counts for replicates
DESeq2
updated 14 days ago by 39k • written 15 days ago by • 0
0
votes
3
replies
78
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GSVA results interpretation
GSVA
updated 13 days ago by ★ 3.0k • written 14 days ago by • 0
0
votes
3
replies
103
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How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 7 days ago by 62k • written 15 days ago by • 0
0
votes
1
reply
78
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How to set threshold of padj value in DeSeq2
DESeq2 padj default
updated 14 days ago by 62k • written 14 days ago by • 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 47k • written 15 days ago by • 0
5
votes
3
replies
286
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Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt ensembldb ensembl
3 months ago • updated 15 days ago jamie.gearing ▴ 60
0
votes
2
replies
111
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Orange point meaning in plotSmear with edgeR
edgeR plotSmear
15 days ago • updated 14 days ago Tess • 0
0
votes
1
reply
66
views
Differential RNA seq on TCGA set
DESeq2 RNASeqData
updated 15 days ago by ★ 2.0k • written 15 days ago by • 0
0
votes
2
replies
92
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microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene
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17 days ago • updated 14 days ago Lluís Revilla Sancho ▴ 700
0
votes
1
reply
63
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Help needed to run PVCA
pvca
updated 15 days ago by 62k • written 15 days ago by • 0
0
votes
1
reply
79
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Cannot download data from IDIES links
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updated 15 days ago by ★ 1.0k • written 4 weeks ago by • 0
1
vote
4
replies
262
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Not able to download recount3 data
recount3
updated 15 days ago by ★ 1.0k • written 5 weeks ago by ▴ 10
2
votes
5
replies
272
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 15 days ago by ★ 1.0k • written 7 weeks ago by • 0
0
votes
1
reply
114
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Recount3 data download problem
recount recount3
updated 15 days ago by ★ 1.0k • written 6 weeks ago by • 0
0
votes
2
replies
217
views
Recount3 error with default "recount3_url" option
recount3
updated 15 days ago by ★ 1.0k • written 8 weeks ago by ▴ 110
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 39k • written 15 days ago by • 0
0
votes
7
replies
269
views
Issue in generating a new DBA object with custom counts
DiffBind dbaobject
5 weeks ago • updated 9 days ago francesco.gandolfi • 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
51
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 15 days ago by ★ 1.3k • written 16 days ago by • 0
0
votes
3
replies
150
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Gene TPM validity with STAR only quantification
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updated 16 days ago by • 0 • written 27 days ago by ▴ 10
5
votes
12
replies
2.9k
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How to annotate gene names for genomic coordinates?
annotation
updated 9 days ago by • 0 • written 7.6 years ago by • 0
0
votes
0
replies
37
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cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
16 days ago cathalgking • 0
0
votes
2
replies
86
views
EpiDISH- from Genomic Cordinate
genomic EpiDISH
updated 16 days ago by • 0 • written 17 days ago by • 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
2
replies
108
views
Time series between two conditions with a common time zero
timeseries
updated 15 days ago by 62k • written 16 days ago by • 0
0
votes
0
replies
51
views
Job: PhD position in Bioinformatics in Jena
Statistics ComputationalBiology Aging MachineLearning
16 days ago alena.vanboemmel • 0
0
votes
1
reply
104
views
Diffbind matrix/batch effect/normalization
DiffBind
updated 16 days ago by ★ 4.6k • written 9 weeks ago by ▴ 10
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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