0
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1
reply
1.5k
views
edgeR MDS plot
RNASeq RNASeq
updated 10.9 years ago by 53k • written 13.9 years ago by ▴ 20
1
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2
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1.8k
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Same number of topTags reported for different contrasts
edger topTags design and contrast matrix
updated 10.9 years ago by 53k • written 10.9 years ago by • 0
0
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2
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Error in BiomaRt package
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10.9 years ago Peter • 0
2
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3
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3.4k
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how to get all information of a platform for all samples using GEOquery
geoquery r
updated 10.9 years ago by 21k • written 10.9 years ago by ▴ 80
1
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7
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6.9k
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convert fastq file to fasta using shortread package
illumina shortread
updated 10.9 years ago by 25k • written 10.9 years ago by • 0
1
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1
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1.5k
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import size factors in deseq2 storage object
deseq2 estimatesizefactors
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 10
0
votes
0
replies
2.1k
views
Trim sequence using R
bioconductor
10.9 years ago kelvinfrog75 • 0
4
votes
5
replies
1.8k
views
Analyzing gene expression data( not celfiles) in limma and annotating results
limma annotation
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ▴ 10
0
votes
1
reply
2.1k
views
DESeq2 -- Bootstrap subsampling to estimate distribution of expression
deseq2 bootstrap differential expression
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 30
0
votes
2
replies
5.8k
views
biomaRt: SNP no access to grch37.ensembl.org
SNP biomart archive grch37
10.9 years ago mrprao • 0
0
votes
0
replies
1.4k
views
Got the following error while working with the DNaseR package; Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : subscript …
dnaser
10.9 years ago martinmullis91 • 0
0
votes
2
replies
2.6k
views
Gviz: Use of transcriptAnnotation in BiomartGeneRegionTrack
gviz
10.9 years ago broder.engler • 0
2
votes
13
replies
3.4k
views
makeTranscriptDbFromBiomart failure from Data Anomaly
biomart genomicfeatures
updated 10.9 years ago by 16k • written 10.9 years ago by ▴ 80
0
votes
2
replies
2.3k
views
BSseq package for Targeted DNA bisulfite sequencing for DMR analysis
methylation DMR analysis
10.9 years ago parker • 0
3
votes
4
replies
4.1k
views
Queries regarding normalization methods for RNA sequencing data analysis
edger
10.9 years ago ash29pathak • 0
2
votes
2
replies
1.9k
views
Non-CpG Methylation in MEDIPS Package
medips
updated 10.9 years ago by ▴ 280 • written 10.9 years ago by • 0
0
votes
9
replies
4.7k
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genomicfeatures rsqlite database or disk is full
genomicfeatures
updated 10.9 years ago by ★ 7.2k • written 10.9 years ago by ▴ 90
13
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9
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9.8k
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Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
10.9 years ago svlachavas ▴ 840
0
votes
0
replies
2.0k
views
Job: Associate Scientist - NGS Informatics @ AstraZeneca (Metro Boston, MA)
cancer translation ngs genomics Job
10.9 years ago jhjohnsn • 0
1
vote
6
replies
2.3k
views
MEDIPS: Output appears to be truncated
medips
updated 10.9 years ago by ▴ 570 • written 10.9 years ago by • 0
2
votes
1
reply
2.2k
views
DESeq2 - test fold change below a threeshold
DESeq2
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 140
2
votes
6
replies
4.9k
views
Combat for batch effects
combat
10.9 years ago zhouxiuqing • 0
1
vote
2
replies
2.0k
views
graphite KEGG pathway list vs KEGG pathway list
graphite
updated 10.9 years ago by ▴ 100 • written 10.9 years ago by • 0
2
votes
8
replies
3.1k
views
DESeq design question
deseq2 design
11.2 years ago • updated 10.9 years ago sunkid • 0
1
vote
5
replies
1.1k
views
matrix design and test advice
rnaseq
updated 10.9 years ago by ★ 29k • written 10.9 years ago by • 0
0
votes
0
replies
1.9k
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missing values in data as input for parody package
parody r NA
10.9 years ago upendrakumar.devisetty • 0
1
vote
3
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2.5k
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QC probes in HTA2-0
affy qc simpleaffy HTA
updated 10.9 years ago by 68k • written 10.9 years ago by ▴ 40
4
votes
9
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4.6k
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Gene expression differential analysis using TCGA dataset
microarray limma
updated 10.9 years ago by ▴ 140 • written 10.9 years ago by • 0
0
votes
1
reply
2.0k
views
tuning memory consumption of summarizeOverlaps?
rna-seq summarizeoverlaps
updated 10.9 years ago by ★ 6.8k • written 10.9 years ago by 6.7k
5
votes
7
replies
4.8k
views
How to specify 'contrast' in glmLRT command when treatments in design matrix are named with numbers, not letters
edger rnaseq glmlrt()
updated 10.9 years ago by 68k • written 10.9 years ago by • 0
1
vote
10
replies
3.4k
views
predictCoding error DNAStringSet_translate
variantannotation predict coding
updated 10.9 years ago by ★ 6.8k • written 10.9 years ago by ▴ 40
0
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1
reply
1.6k
views
Subsequent analysis after PCA and sample distance matrix-Outliers?
deseq deseq2
updated 10.9 years ago by 43k • written 10.9 years ago by • 0
1
vote
4
replies
2.8k
views
ChIPQC: reads counts in bam do not match ones from samtools flagstat
chipqc
updated 10.9 years ago by ▴ 420 • written 10.9 years ago by • 0
1
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3
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2.0k
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BioNet package network analysis important questions for tutorial
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10.9 years ago svlachavas ▴ 840
5
votes
9
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4.4k
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Merge different datasets regarding a common number of DE genes in R
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10.9 years ago svlachavas ▴ 840
1
vote
2
replies
2.0k
views
Question about the proper way to combine Illumina Human HT-12 v4 expression datasets from different labs
combat batch effect
10.9 years ago jaro.slamecka ▴ 140
1
vote
1
reply
1.7k
views
DeSeq2 Multiple Conditons
deseq2 multiple factor design
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 10
2
votes
4
replies
9.6k
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DESEQ2 results and contrast (and a relevel question)
deseq deseq2
10.9 years ago yg • 0
0
votes
3
replies
2.9k
views
problem with cbind on GRanges object - new bug?
genomicranges cbind
10.9 years ago Janet Young ▴ 740
3
votes
2
replies
2.3k
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How are autofluorescence values used in the spillover/compensate functions?
flowcore flow cytometry compensation spillover
updated 10.9 years ago by ▴ 150 • written 10.9 years ago by ▴ 20
0
votes
1
reply
1.0k
views
several gene names for a probeID in affymetrix annotation file
affy annotation
updated 10.9 years ago by 68k • written 10.9 years ago by • 0
0
votes
1
reply
2.3k
views
DEXSeq with multiple conditions
dexseq alternative splicing exon skipping
updated 10.9 years ago by ★ 3.8k • written 10.9 years ago by • 0
0
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5
replies
3.1k
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loadGSC() Piano package
piano
updated 10.9 years ago by ▴ 70 • written 10.9 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Deseq2 and gene clustering
deseq2 clustering
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 40
0
votes
6
replies
9.8k
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Deseq2 supervised heatmap
deseq2 supervised
10.9 years ago aristotele_m ▴ 40
3
votes
5
replies
2.7k
views
PCA of voom weight values
limma voom rnaseq
updated 10.9 years ago by 53k • written 10.9 years ago by ▴ 140
0
votes
5
replies
2.3k
views
News: Ensembl 79 release is out!
Ensembl biomart release news News
updated 10.9 years ago by ★ 8.2k • written 10.9 years ago by ▴ 20
0
votes
0
replies
1.6k
views
News: OmicCircos was updated
visualization omiccircos News
10.9 years ago Hu, Ying NIH/NCI [E] ▴ 50
0
votes
2
replies
1.8k
views
RCircos 2D track plot for a small region of genome
BSgenome BSgenome BSgenome BSgenome
updated 10.9 years ago by ▴ 50 • written 12.1 years ago by ★ 13k
1
vote
3
replies
1.9k
views
OmicCircos mapping data file.
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updated 10.9 years ago by ▴ 50 • written 11.2 years ago by ▴ 60
46,735 results • Page 466 of 935
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Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice by Gordon Smyth 53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
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Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
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