1
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4
replies
1.4k
views
CAGEr quantilePositions() takes forever to run
CAGEr quantilePositions
5.7 years ago mirkocelii ▴ 40
0
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1
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945
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DESeq2 for normalizing metagenomic counts
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
reply
538
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plot function in flowType under R4.0.0
software error
5.7 years ago lifengt • 0
0
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2
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626
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How to find differential gene and expression analysis using DESeq or edgeR
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updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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2
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669
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about function parameters
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updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
1
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8
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How to change XLOC ID to Gene symbol from Cuffdiff ?
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updated 4.0 years ago by • 0 • written 5.7 years ago by • 0
0
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4
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2.0k
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Error attaching TIN
software error GO.db TIN
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
1
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1
reply
797
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Meeting Questions when using Deseq2paper package
deseq2
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
0
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0
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1.1k
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How to overlap heatmaps on Gviz?
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5.7 years ago kris.petrini • 0
0
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1
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2.3k
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Error while installing GSVA
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updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 10
2
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7
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1.2k
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lfcShrink giving error
deseq2
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 10
0
votes
1
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1.4k
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error when forging a BSgenome
BSgenome
updated 5.7 years ago by 4.3k • written 5.7 years ago by ▴ 10
4
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7
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6.2k
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Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
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updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
0
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4
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2.1k
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scran's quickCluster error
scran
updated 5.7 years ago by ★ 29k • written 5.7 years ago by • 0
0
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0
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1.4k
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ChIPseeker error when I wnat to get tagMatrix
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5.7 years ago hfyuan2016 • 0
0
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8
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1.7k
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To start organising data for DESeq2
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updated 5.7 years ago by ★ 1.4k • written 5.7 years ago by ▴ 10
0
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9
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2.8k
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i can't install metade package
software error
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
23
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11
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Bioconductor vs BioConductor
project
updated 5.7 years ago by 53k • written 5.7 years ago by ▴ 40
1
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7
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3.3k
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tximport from RSEM expected counts: is it possible to import from a table rather than a file?
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updated 4.8 years ago by • 0 • written 5.7 years ago by ▴ 60
0
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2
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1.1k
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Extraction of individual results from DESeq2 data
deseq2
updated 5.7 years ago by ★ 1.4k • written 5.7 years ago by • 0
0
votes
1
reply
555
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Server disk full for archived biomaRt database
software error
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
1
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5
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4.1k
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Updating Out of Date BiocManager Packages
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updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
1
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1
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736
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RMarkdown in combination with OUTRIDER
software error
updated 3.0 years ago by • 0 • written 5.7 years ago by ▴ 10
0
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1
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1.1k
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
5.7 years ago AishaD • 0
1
vote
1
reply
773
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correct use of regularized log/VST values from deseq2
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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7
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4.0k
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High padj in DESeq2
deseq2 RNA-seq microRNA
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 10
2
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6
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2.1k
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Nested design matrix in edgeR
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updated 5.7 years ago by 53k • written 5.7 years ago by • 0
0
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0
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1.1k
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Subset samples expressing genes for DEXSeq or DRIMSeq analysis
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5.7 years ago alexis.weinreb • 0
0
votes
0
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965
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Correcting for multiple comparisons in permutation procedure using multtest
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5.7 years ago john.gordon.yellow • 0
0
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0
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1.4k
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listSRAfile: Error in if (is.na(sra_acc$run[i])) { : argument is of length zero
SRAdb
5.7 years ago Aditya ▴ 160
0
votes
4
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1.4k
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ProFIA package error for noise estimation
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updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
0
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1
reply
537
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How to design block vector for duplicateCorrelation()
limma
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
2
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4
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MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
1
vote
6
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2.0k
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Behaviour of getCTSS on a CAGEset - extra reads?
cager cage ctss
updated 5.7 years ago by ▴ 180 • written 6.5 years ago by ▴ 20
0
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2
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1.6k
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How to create GRanges for TES
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updated 5.7 years ago by ★ 11k • written 5.7 years ago by ▴ 10
0
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3
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2.0k
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PureCN gene LOH very common, amp/del not
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updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
3
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4
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1.3k
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Correct input data for avereps function (for averaging multiple probes for same gene)
limma
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
5
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2
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3.0k
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How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
1
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5
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3.5k
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Peer's Certificate issuer is not recognized
BioMart
updated 5.7 years ago by ★ 6.6k • written 5.7 years ago by • 0
0
votes
2
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1.5k
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Gviz AlignmentsTrack: how to prevent reads from overlapping each other
Gviz
updated 5.7 years ago by ▴ 750 • written 5.7 years ago by • 0
0
votes
5
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1.8k
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Error with DESeqDataSetFromHTSeqCount
DESeqDataSetFromHTSeqCount
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
0
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4
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1.6k
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How to use ggcyto_arrange to plotframes in a frameset in a new order
ggcyto ggcyto_arrange autoplot
updated 5.7 years ago by ▴ 310 • written 5.7 years ago by ▴ 30
1
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1
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2.4k
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
4
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5
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2.8k
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makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
1
reply
1.1k
views
Is there an easy way to do pos(x) <- pos(x) + 1 for a GPos object ?
GenomicRanges GPos
5.7 years ago Charles Plessy ▴ 180
0
votes
0
replies
1.2k
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Potential oversimplification in the overlap function
ChIPseeker
5.7 years ago konsta.kukkonen • 0
0
votes
1
reply
1.0k
views
RSAMTOOLS to analyse BED FILES
RSAMTOOLS BED-FILE
5.7 years ago r.mulder01 • 0
0
votes
0
replies
1.0k
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readGenbank can't handle multiple contigs?
genbankr parsing
5.7 years ago sean.c.m.booth • 0
1
vote
3
replies
1.3k
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CAGEr: Quantile Values (q_0.1 and q_0.9) in CAGEset / CAGEexp objects
CAGEr CAGEset quantile CAGEexp
5.7 years ago mirkocelii ▴ 40
2
votes
4
replies
1.4k
views
MEDIPS results differ with sample ordering
MEDIPS edgeR
updated 5.7 years ago by ▴ 570 • written 6.0 years ago by ▴ 60
46,717 results • Page 166 of 935
Recent ...
Replies
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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