Showing : MEDIPS • reset
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How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?
R Medips edgeR
updated 9.6 years ago by ▴ 570 • written 9.6 years ago by • 0
2
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1
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1.5k
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How createSet from reduced "paire-ed" sequencing on MeDIPS?
medips R input files
updated 9.6 years ago by ▴ 570 • written 9.6 years ago by • 0
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1
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1.3k
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MEDIPS stable version problem
MEDIPS
updated 9.6 years ago by ▴ 570 • written 9.7 years ago by • 0
2
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2
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1.9k
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Normalizing Depth Coverage between samples MEDIPS
normalization medips depth edgeR "R"
updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
2
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13
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3.1k
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Error with MEDIPS.createSet in queryHits
medips createset
9.9 years ago • updated 9.8 years ago Vanilla • 0
0
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2
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1.5k
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New to R: How to use your own data for Bioconductor Packages
MEDIPS rsamtools
updated 10.0 years ago by ★ 8.2k • written 10.0 years ago by • 0
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1
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1.1k
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MEDIPS test data lack of 4 files
medips
updated 10.1 years ago by ▴ 570 • written 10.1 years ago by • 0
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2
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2.6k
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MEDIPS vs MACS: why does MEDIPS generate more conservative p-values
p-value medips MACS
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by • 0
0
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2
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1.5k
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MEDIPS: Any way to get more columns/data from MEDIPS.mergeFrames?
MEDIPS mergeFrames
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by • 0
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2
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1.9k
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MEDIPS - RPKM
MEDIPS
10.5 years ago malbert1 • 0
0
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1
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1.3k
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MEDIPS : Populating fragments from Paired End reads
medips
updated 10.5 years ago by ▴ 570 • written 10.5 years ago by • 0
2
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2
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1.8k
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Non-CpG Methylation in MEDIPS Package
medips
updated 10.5 years ago by ▴ 280 • written 10.5 years ago by • 0
1
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6
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2.1k
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MEDIPS: Output appears to be truncated
medips
updated 10.5 years ago by ▴ 570 • written 10.5 years ago by • 0
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2
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1.7k
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Bioconductor source code - Errno::ECONNREFUSED in Codes#show
medips bioconductor error source code
10.8 years ago malbert1 • 0
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2
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MEDIPS: Export rms values as Wiggle for visualization in UCSC
medips
10.9 years ago malbert1 • 0
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1
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2.0k
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MEDIPS quality control
process medips
updated 10.9 years ago by ▴ 570 • written 11.0 years ago by • 0
0
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9
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3.1k
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MEDIPS: how does MEDIPS define a methylated region / cluster?
Sequencing MEDIPS
updated 10.9 years ago by • 0 • written 11.0 years ago by ★ 13k
0
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5
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2.5k
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How does MEDIPS handle multiple mapping of a read
MEDIPS MEDIPS
updated 11.0 years ago by ▴ 570 • written 11.0 years ago by ★ 13k
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3
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8.4k
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Downgrading R to an older version
MEDIPS ChAMP MEDIPS ChAMP
updated 11.1 years ago by ★ 8.2k • written 11.1 years ago by ▴ 70
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1
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2.3k
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edgeR: Analyze mini-time-series MeDIP data of pooled DNAs without replicates?
Sequencing edgeR MEDIPS Sequencing edgeR MEDIPS
11.1 years ago Vang Le ▴ 80
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1
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1.6k
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non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ★ 13k
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2
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2.0k
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mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 11.3 years ago by ▴ 280 • written 11.3 years ago by ▴ 10
0
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1
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2.4k
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It works! RE: So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer
updated 11.4 years ago by ▴ 570 • written 11.4 years ago by ▴ 220
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1
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2.0k
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So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer
updated 11.4 years ago by ▴ 570 • written 11.4 years ago by ▴ 220
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5
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2.4k
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Rsamtools filtering bam file: RE: MEDIPS.createSet error
GO BSgenome BSgenome Rsamtools genomes MEDIPS GO BSgenome BSgenome Rsamtools genomes
updated 11.5 years ago by 25k • written 11.5 years ago by ▴ 220
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2
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1.5k
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MEDIPS.createSet error
BSgenome BSgenome Rsamtools MEDIPS BSgenome BSgenome Rsamtools MEDIPS
updated 11.5 years ago by ▴ 570 • written 11.5 years ago by ▴ 220
0
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5
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2.6k
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MEDIPS.createSet error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 11.5 years ago by ▴ 570 • written 11.5 years ago by ▴ 220
0
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1
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1.9k
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[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 11.7 years ago by ▴ 280 • written 11.7 years ago by ▴ 10
0
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2
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2.2k
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[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 20
0
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2
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1.8k
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Aha: different error may be a clue: RE: separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
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6
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2.2k
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separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
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3
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1.6k
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separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
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0
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1.2k
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It works: RE: using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
11.7 years ago Vining, Kelly ▴ 220
0
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1
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1.5k
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using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
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1
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5.6k
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Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 11.7 years ago by ▴ 280 • written 11.7 years ago by 16k
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0
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2.4k
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BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
11.8 years ago Hervé Pagès 16k
0
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1
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1.4k
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MEDIPS rms normalization by input
Coverage MEDIPS Coverage MEDIPS
updated 11.9 years ago by ▴ 570 • written 11.9 years ago by ★ 13k
0
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2
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1.5k
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MEDIPS
Coverage MEDIPS Coverage MEDIPS
updated 11.9 years ago by ▴ 570 • written 11.9 years ago by ▴ 350
0
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1
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1.2k
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MEDIPS saturation error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 12.0 years ago by ▴ 40 • written 12.0 years ago by ★ 13k
0
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3
replies
3.3k
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MEDIPS, GRanges, IRanges error processing BAM file
Alignment BSgenome PROcess BSgenome IRanges MEDIPS Alignment BSgenome PROcess BSgenome
updated 12.1 years ago by ▴ 570 • written 12.1 years ago by ▴ 40
0
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2
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1.3k
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MEDIPS no longer producing AMS values
Sequencing MEDIPS Sequencing MEDIPS
updated 12.1 years ago by ▴ 570 • written 12.1 years ago by ▴ 40
0
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4
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1.4k
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I need BSgenome for Eucalyptus grandis
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 12.1 years ago by ★ 7.2k • written 12.1 years ago by ★ 13k
0
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0
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890
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MEDIPS differential coverage
Coverage MEDIPS Coverage MEDIPS
12.3 years ago Sara Castelletti ▴ 40
0
votes
7
replies
2.1k
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MEDIPS error extending reads
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 12.4 years ago by ▴ 570 • written 12.4 years ago by ▴ 290
0
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1
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1.4k
views
MEDIPS
Sequencing Alignment MEDIPS Sequencing Alignment MEDIPS
updated 12.4 years ago by ▴ 570 • written 12.4 years ago by ▴ 350
0
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1
reply
1.6k
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Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 12.5 years ago by ▴ 570 • written 12.5 years ago by ▴ 290
0
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2
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1.4k
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Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray Preprocessing BSgenome BSgenome MEDIPS Microarray Preprocessing BSgenome MEDIPS
updated 12.6 years ago by ▴ 290 • written 12.6 years ago by ▴ 570
4
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2
replies
1.8k
views
MEDIPS
MEDIPS MEDIPS
12.6 years ago Paolo Kunderfranco ▴ 350
0
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0
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928
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Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray BSgenome BSgenome MEDIPS Microarray BSgenome BSgenome MEDIPS
12.6 years ago Stephen Turner ▴ 290
0
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2
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1.9k
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Building custom genome in MeDIPS
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 13.0 years ago by 68k • written 13.0 years ago by ▴ 10
105 results • Page 2 of 3
Recent ...
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Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
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I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
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> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
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The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
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