Showing : Sequencing • reset
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[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 11.0 years ago by ★ 13k • written 11.0 years ago by ▴ 330
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14
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3.4k
views
Trimming of partial adaptor sequences
Sequencing Cancer Biostrings Sequencing Cancer Biostrings
10.8 years ago Taylor, Sean D ▴ 250
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13
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2.7k
views
multiple hits with countOverlaps function
Sequencing GenomicFeatures Sequencing GenomicFeatures
13.0 years ago Wei Shi ★ 3.6k
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12
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2.0k
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Job offer at EMBL Heidelberg
Sequencing Sequencing
updated 15.3 years ago by ▴ 20 • written 15.3 years ago by ★ 1.2k
2
votes
11
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1.9k
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DESeq2 polysome profiling analysis with 2 interaction terms
deseq2 sequencing polysome profiling
updated 6.9 years ago by 41k • written 6.9 years ago by ▴ 10
0
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10
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1.9k
views
Statistics for next-generation sequencing transcriptomics
Sequencing SAGE Sequencing SAGE
updated 14.8 years ago by ▴ 10 • written 14.8 years ago by ★ 3.4k
1
vote
10
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2.1k
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Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 10
0
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9
replies
2.3k
views
SOLiD color space data
Sequencing Sequencing
updated 13.4 years ago by ▴ 500 • written 13.4 years ago by ▴ 460
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9
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2.5k
views
MEDIPS: how does MEDIPS define a methylated region / cluster?
Sequencing MEDIPS
updated 9.6 years ago by • 0 • written 9.6 years ago by ★ 13k
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8
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2.3k
views
DEXSeq - too many exons in gene
Sequencing Annotation DEXSeq Sequencing Annotation DEXSeq
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 490
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8
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1.6k
views
Designing a model with blocking and other interactions
Sequencing Sequencing
updated 10.1 years ago by 50k • written 10.1 years ago by ▴ 110
0
votes
8
replies
1.6k
views
Single nucleotide based RNAseq normalization with edgeR
Sequencing RNASeq Normalization edgeR Sequencing RNASeq Normalization edgeR
updated 13.2 years ago by ▴ 20 • written 13.2 years ago by 50k
3
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8
replies
4.4k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 7.7 years ago by • 0 • written 10.3 years ago by ★ 13k
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7
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2.7k
views
[ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Sequencing ReportingTools DESeq2 Sequencing ReportingTools DESeq2
updated 10.3 years ago by 65k • written 10.3 years ago by ▴ 30
0
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7
replies
1.3k
views
SNP 6 chip
SNP Sequencing affy SNP Sequencing affy
updated 12.5 years ago by 65k • written 12.5 years ago by ▴ 210
0
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7
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2.2k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 7.7 years ago by • 0 • written 14.0 years ago by ★ 1.6k
0
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6
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1.4k
views
pileupAsGRanges depth limit
Sequencing ggbio Sequencing ggbio
updated 11.4 years ago by 25k • written 11.4 years ago by ★ 1.1k
6
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6
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1.4k
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
2.5 years ago ary.lech ▴ 10
0
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6
replies
6.9k
views
DeSeq vs current version of Cuffdiff
Sequencing Bayesian Cancer DESeq Sequencing Bayesian Cancer DESeq
updated 12.2 years ago by ▴ 290 • written 12.2 years ago by ★ 2.0k
0
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6
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1.5k
views
need help for the study design of a RNA-Seq project
SNP Sequencing SNP Sequencing
11.0 years ago shirley zhang ★ 1.0k
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6
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1.2k
views
exon exon junction library for human
Sequencing Sequencing
updated 14.7 years ago by ★ 13k • written 14.7 years ago by ★ 1.0k
0
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5
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1.8k
views
edgeR for data combined from different studies and/or platforms
Sequencing Cancer edgeR Sequencing Cancer edgeR
updated 11.1 years ago by ★ 7.9k • written 11.1 years ago by ★ 13k
2
votes
5
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1.4k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
20 months ago Marcus • 0
0
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5
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2.0k
views
downloading different kinds of microarray data
Sequencing Microarray Genetics Annotation gpls convert GEOquery GEOmetadb Sequencing gpls
updated 13.7 years ago by ▴ 30 • written 13.7 years ago by 21k
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5
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2.2k
views
getting sample size for RNAseq experiment
rnaseqpower sspa sample size sequencing complex-design
updated 8.2 years ago by ▴ 20 • written 8.2 years ago by • 0
0
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5
replies
1.6k
views
EasyRNAseq - error in building count table - Error in unlist
Sequencing RNASeq edgeR easyRNASeq Sequencing RNASeq edgeR easyRNASeq
updated 10.6 years ago by ★ 1.2k • written 10.6 years ago by ★ 13k
2
votes
5
replies
1.6k
views
DEXSeq update results change
Sequencing DESeq DEXSeq Sequencing DESeq DEXSeq
9.7 years ago António Miguel de Jesus Domingues ▴ 490
0
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5
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1.5k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 10.7 years ago by ★ 6.8k • written 10.7 years ago by ▴ 300
2
votes
4
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6.9k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 8.9 years ago by • 0 • written 9.9 years ago by ★ 13k
0
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4
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1.3k
views
finding a very large number of false positives using edgeR
Sequencing RNASeq edgeR Sequencing RNASeq edgeR
updated 10.3 years ago by 50k • written 10.3 years ago by ▴ 20
0
votes
4
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1.5k
views
Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Network
updated 13.0 years ago by ▴ 310 • written 13.0 years ago by ★ 8.2k
0
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4
replies
1.5k
views
faster way to get differential calls from pileup?
SNP Sequencing PROcess SNP Sequencing PROcess
updated 13.5 years ago by 21k • written 13.5 years ago by ▴ 260
0
votes
4
replies
2.8k
views
DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.1 years ago Henrik Bengtsson ★ 2.4k
2
votes
4
replies
1.4k
views
Complex ANOVA analysis in EdgeR
edger anova sequencing
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
6
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4
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1.5k
views
How to normalize chemical genomics barcode sequencing data
limma normalization sequencing edger
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
0
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4
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1.2k
views
Query
Sequencing Sequencing
updated 14.2 years ago by 25k • written 14.2 years ago by ▴ 10
0
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4
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1.7k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
12.2 years ago delhomme@embl.de ★ 1.2k
0
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4
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1.4k
views
Regarding multiple hits of same read
Sequencing Sequencing
updated 10.6 years ago by ★ 13k • written 10.6 years ago by ▴ 170
0
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4
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1.7k
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segfault for pairwiseAlignment
sequencing software error alignment
updated 9.6 years ago by ★ 6.5k • written 9.6 years ago by ▴ 10
0
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4
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1.2k
views
Course material for "Using Bioconductor for ChIP-seq experiments"
Sequencing Cancer BSgenome annotate Biostrings BSgenome Sequencing Cancer BSgenome
updated 15.4 years ago by ▴ 10 • written 15.4 years ago by ★ 1.6k
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4
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1.1k
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Opinions on array design, normalization, and linear modeling with LIMMA
Sequencing Coverage Normalization limma Sequencing Coverage Normalization limma
updated 16.5 years ago by ▴ 60 • written 16.5 years ago by ▴ 890
0
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4
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1.5k
views
Converting data into MAlist to use in LIMMA
Sequencing Microarray Annotation Normalization affy convert Sequencing Microarray affy
updated 14.2 years ago by ★ 1.9k • written 14.2 years ago by ▴ 60
3
votes
4
replies
3.4k
views
Variance filtering prior to RNA-seq differential expression
sequencing deseq limma
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 420
0
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4
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1.4k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
13.6 years ago heyi xiao ▴ 360
0
votes
4
replies
8.1k
views
DESeq adjusted pvalue calculation / filtering data
Sequencing Organism qvalue DESeq Sequencing Organism qvalue DESeq
updated 12.4 years ago by ★ 6.0k • written 12.4 years ago by ▴ 20
0
votes
4
replies
1.6k
views
IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 8.4 years ago by ★ 6.5k • written 8.4 years ago by • 0
0
votes
3
replies
1.9k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
10.7 years ago Rory Stark ★ 5.2k
0
votes
3
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1.2k
views
Lapply for two GRanges objects?
Sequencing Cancer Sequencing Cancer
updated 13.1 years ago by 25k • written 13.1 years ago by ▴ 260
0
votes
3
replies
1.1k
views
help - where to start
Sequencing Sequencing
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 330
0
votes
3
replies
987
views
(EdgeR) statistical justification of partitioning dataset for multiple analysis
Sequencing edgeR Sequencing edgeR
updated 10.2 years ago by ★ 7.9k • written 10.2 years ago by ▴ 90
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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