Showing : Alignment • reset
0
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SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq quasr alignment
updated 10.2 years ago by ▴ 400 • written 10.2 years ago by • 0
0
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1
reply
2.2k
views
Counting SNPs where ambiguity codes represent heterozygosity.
Biostrings SNPs alignment
updated 10.5 years ago by 16k • written 10.6 years ago by ▴ 30
0
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2
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4.5k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 10.6 years ago by • 0 • written 12.8 years ago by ★ 8.2k
0
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6
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4.1k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 10.6 years ago by 16k • written 10.6 years ago by ▴ 70
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2.2k
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Clustering sequence on similarity using percentage identity matrix
alignment clustering
10.6 years ago Bade ▴ 310
2
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4
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8.1k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 10.7 years ago by • 0 • written 11.7 years ago by ★ 13k
1
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0
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1.8k
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Genome editing analysis with Illumina sequencing
indel sequencing alignment
10.8 years ago Merienne Nicolas ▴ 120
5
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8
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7.4k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
11.0 years ago ben.ward ▴ 30
5
votes
12
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8.8k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 11.0 years ago by 53k • written 11.8 years ago by ★ 1.0k
3
votes
3
replies
2.2k
views
Reading large DNA alignments and keeping polymorphic sites
sequence alignment biostrings
updated 11.1 years ago by 16k • written 11.2 years ago by ▴ 30
1
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2
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2.9k
views
Finding mismatches between reads and reference sequence
bsgenome cigar alignment
updated 11.2 years ago by 16k • written 11.2 years ago by ▴ 40
6
votes
3
replies
2.6k
views
Possible bug in Rsubread Phred-Score read
rsubread bug alignment
updated 11.2 years ago by ★ 3.6k • written 11.2 years ago by ▴ 20
0
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1
reply
1.8k
views
Blast K and Lambda
alignment
11.3 years ago haifengc • 0
0
votes
4
replies
2.1k
views
segfault for pairwiseAlignment
sequencing software error alignment
updated 11.4 years ago by ★ 6.5k • written 11.4 years ago by ▴ 10
0
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3
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1.8k
views
edgeR: mixing technical replicates from Illumina HiSeq and MiSeq
Sequencing Alignment GO edgeR DESeq2
updated 11.4 years ago by ★ 7.9k • written 11.4 years ago by ▴ 60
0
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0
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1.6k
views
Question on Gviz
Alignment Gviz
11.4 years ago florian.hahne@novartis.com ★ 1.6k
0
votes
0
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1.5k
views
edgeR: mixing technical replicates from Illumina HiSeq and MiSeq
Sequencing Alignment GO edgeR DESeq2 Sequencing Alignment GO edgeR DESeq2
11.4 years ago Gordon Smyth 53k
0
votes
4
replies
2.3k
views
nearly exact overlaps between GAlignmentPairs and GenomicRanges
Alignment Alignment
11.5 years ago Georg Otto ▴ 120
0
votes
1
reply
1.4k
views
Putative bug in Biostrings
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 11.6 years ago by ▴ 10 • written 11.6 years ago by 16k
0
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1
reply
2.1k
views
Biostrings readDNAMultipleAlignment broken for fasta input
Alignment Biostrings Alignment Biostrings
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 740
0
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8
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4.0k
views
Annotation files for bacterial genome RNAseq
Alignment Annotation ASSIGN Alignment Annotation ASSIGN
updated 11.6 years ago by 68k • written 11.6 years ago by ▴ 80
0
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3
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2.8k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Alignment DESeq2 Alignment DESeq2
updated 11.7 years ago by 43k • written 11.7 years ago by ▴ 30
0
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0
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1.6k
views
Please revise this edgeR code
Alignment Organism topGO edgeR Alignment Organism topGO edgeR
11.8 years ago biotech ▴ 160
0
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0
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1.8k
views
Is this edgeR code OK?
Alignment Organism topGO edgeR Alignment Organism topGO edgeR
11.8 years ago biotech ▴ 160
0
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1
reply
2.5k
views
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 11.8 years ago by ▴ 570 • written 11.8 years ago by ▴ 220
0
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5
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2.3k
views
A question about the function readGAlignmentPairs in GenomicRnages package
Alignment Cancer convert GenomicAlignments Alignment Cancer convert GenomicAlignments
updated 11.8 years ago by 16k • written 11.9 years ago by ▴ 50
0
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1
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2.1k
views
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 11.9 years ago by ▴ 570 • written 11.9 years ago by ▴ 220
0
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1
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1.4k
views
countOverlaps gives an empty SummarizeExperiments
RNASeq Alignment biomaRt rtracklayer DESeq RNASeq Alignment biomaRt rtracklayer DESeq
updated 11.9 years ago by 25k • written 11.9 years ago by ★ 13k
0
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5
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2.8k
views
MEDIPS.createSet error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 11.9 years ago by ▴ 570 • written 11.9 years ago by ▴ 220
0
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0
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1.2k
views
Question on Gviz
Alignment Gviz Alignment Gviz
11.9 years ago florian.hahne@novartis.com ★ 1.6k
0
votes
7
replies
2.7k
views
QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
Alignment Rattus norvegicus BSgenome BSgenome QuasR Alignment Rattus norvegicus BSgenome
updated 11.9 years ago by 16k • written 11.9 years ago by ★ 4.1k
0
votes
3
replies
1.5k
views
The ambiguous alignment examples in findMateAlignment don't have to be dumped
Alignment Alignment
updated 12.0 years ago by 16k • written 12.0 years ago by ▴ 20
0
votes
2
replies
1.9k
views
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 12.1 years ago by ▴ 570 • written 12.1 years ago by ▴ 220
0
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6
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2.3k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 12.1 years ago by ▴ 570 • written 12.1 years ago by ▴ 220
0
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1
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2.7k
views
Pairwise Alignment on Large Protein Sequence Data Set
Alignment genomes Alignment genomes
updated 12.1 years ago by 16k • written 12.1 years ago by ★ 13k
0
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4
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2.1k
views
WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)
Alignment Alignment
updated 12.3 years ago by ★ 11k • written 12.3 years ago by ▴ 40
2
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1
reply
2.7k
views
Sequence Distance matrix with large sequences
Alignment Alignment
updated 12.3 years ago by 16k • written 12.3 years ago by ▴ 20
0
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2
replies
7.4k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 12.3 years ago by ★ 11k • written 12.3 years ago by 16k
1
vote
1
reply
3.4k
views
Creat PWM from Alignment with Gaps
Alignment Cancer Alignment Cancer
updated 12.3 years ago by ▴ 250 • written 12.4 years ago by 16k
0
votes
1
reply
1.3k
views
Rsamtools: readGAlignmentsFromBam weird behavior reading MAPQ and RNEXT fields
Alignment Alignment
updated 12.3 years ago by 16k • written 12.3 years ago by ★ 13k
0
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2
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1.5k
views
Fwd: BioStrings PairwiseAlignment deletion() insertion() function
Alignment Cancer Biostrings IRanges Alignment Cancer Biostrings IRanges
updated 12.4 years ago by ▴ 30 • written 12.4 years ago by 16k
0
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16
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2.8k
views
readGAlignmentPairs error
Alignment Alignment
updated 12.4 years ago by 16k • written 12.4 years ago by ▴ 90
0
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0
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1.0k
views
BioStrings PairwiseAlignment deletion() insertion() function
Alignment Alignment
12.4 years ago Marcin Imielinski ▴ 30
0
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1
reply
1.3k
views
readGappedAlignments and param argument
Alignment Alignment
updated 12.4 years ago by 25k • written 12.4 years ago by ▴ 10
1
vote
1
reply
1.6k
views
Rsubread for paired end SOLID sequencing
Sequencing Alignment convert Rsubread Sequencing Alignment convert Rsubread
updated 12.4 years ago by ★ 3.6k • written 12.4 years ago by ▴ 50
0
votes
1
reply
1.2k
views
MEDIPS saturation error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 12.4 years ago by ▴ 40 • written 12.4 years ago by ★ 13k
0
votes
0
replies
2.6k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
12.4 years ago Sarah Pohl ▴ 30
1
vote
3
replies
2.4k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment
updated 12.5 years ago by ★ 7.2k • written 12.5 years ago by ▴ 220
0
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0
replies
939
views
test for overlap
Alignment Alignment
12.5 years ago Adrian Johnson ▴ 330
0
votes
2
replies
3.7k
views
Rsamtools: sortBam() and 'samtools sort' does not give the same results
Alignment Rsamtools Alignment Rsamtools
updated 12.5 years ago by 25k • written 12.5 years ago by ★ 2.4k
208 results • Page 2 of 5
Recent ...
Replies
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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