Showing : Alignment • reset
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MEDIPS, GRanges, IRanges error processing BAM file
Alignment BSgenome PROcess BSgenome IRanges MEDIPS Alignment BSgenome PROcess BSgenome
updated 12.3 years ago by ▴ 570 • written 12.3 years ago by ▴ 40
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job advertisement
Genetics Alignment Visualization Genetics Alignment Visualization
12.4 years ago Zhenyu Xu ▴ 10
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views
filterBam
Alignment Alignment
updated 12.4 years ago by ▴ 500 • written 12.4 years ago by ▴ 500
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ReportingTools: formatting html report
Alignment ReportingTools Alignment ReportingTools
12.5 years ago Gabriel Becker ▴ 70
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5
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obtaining a complete global alignment via pairwiseAlignment
Alignment GO Cancer BSgenome BSgenome Alignment GO Cancer BSgenome BSgenome
updated 12.5 years ago by 25k • written 12.5 years ago by ★ 13k
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3
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DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 12.5 years ago by 43k • written 12.5 years ago by ▴ 150
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Howto annotate blast subject.id with AnnotationDbi
Alignment GO annotate AnnotationDbi Alignment GO annotate AnnotationDbi
updated 12.5 years ago by ★ 7.2k • written 12.5 years ago by ▴ 40
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views
DEXSeq Problems
Alignment Homo sapiens PROcess Alignment Homo sapiens PROcess
updated 12.5 years ago by ★ 3.8k • written 12.5 years ago by ▴ 150
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multiple feature/mode counting with summarizeOverlaps
Alignment Alignment
12.5 years ago Thomas Girke ★ 1.7k
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tutorials for RNA-seq analysis in Bioconductor
Alignment Alignment
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ▴ 70
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views
QuasR special case alignment
Alignment genomes QuasR Alignment genomes QuasR
updated 12.6 years ago by ▴ 340 • written 12.6 years ago by ▴ 350
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Deleting object rows while looping - II
Coverage Alignment Cancer PROcess Coverage Alignment Cancer PROcess
updated 12.6 years ago by ★ 13k • written 12.6 years ago by 16k
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views
Deleting object rows while looping - II
Coverage Alignment PROcess Coverage Alignment PROcess
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 90
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QuasR special case alignment
Alignment QuasR Alignment QuasR
updated 12.6 years ago by ▴ 350 • written 12.6 years ago by ▴ 340
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reply
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views
multiple threads on QuasR
Alignment GLAD QuasR Alignment GLAD QuasR
12.6 years ago Michael Stadler ▴ 350
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1.2k
views
loss of stranding in alignments from recent versions of Rsubread
Alignment Alignment
updated 12.6 years ago by ★ 3.6k • written 12.6 years ago by ★ 4.2k
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7
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2.2k
views
MEDIPS error extending reads
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 12.6 years ago by ▴ 570 • written 12.6 years ago by ▴ 290
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BitSeq transcript IDs
Alignment PROcess BitSeq Alignment PROcess BitSeq
updated 12.7 years ago by ▴ 30 • written 12.7 years ago by ▴ 70
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views
MEDIPS
Sequencing Alignment MEDIPS Sequencing Alignment MEDIPS
updated 12.7 years ago by ▴ 570 • written 12.7 years ago by ▴ 350
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reply
1.4k
views
BitSeq getExpression crash
Alignment PROcess BitSeq Alignment PROcess BitSeq
updated 12.7 years ago by ▴ 70 • written 12.7 years ago by ▴ 30
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5
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Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 12.8 years ago by ▴ 420 • written 12.8 years ago by ★ 11k
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5
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DiffBind error
Alignment DiffBind Alignment DiffBind
updated 12.8 years ago by ★ 5.2k • written 12.8 years ago by ▴ 280
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8.3k
views
BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 2.0 years ago by • 0 • written 12.9 years ago by ▴ 280
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1
reply
1.8k
views
Minimal input data format for bsseq
Sequencing Alignment bsseq Sequencing Alignment bsseq
updated 12.9 years ago by ★ 6.5k • written 12.9 years ago by ▴ 20
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EdgeR estimateTagwiseDisp()
Alignment edgeR Alignment edgeR
updated 13.0 years ago by 53k • written 13.0 years ago by ★ 13k
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readAligned with bowtie2 input
Alignment Cancer ShortRead Alignment Cancer ShortRead
13.0 years ago Martin Morgan 25k
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readAligned with bowtie2 input
Alignment ShortRead Alignment ShortRead
13.0 years ago Maria Dermit ▴ 10
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get synthetic exon dataset with easyRNASeq
RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO
13.1 years ago delhomme@embl.de ★ 1.2k
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bug in Biostrings mismatchTable?
Alignment Alignment
updated 13.1 years ago by 16k • written 13.1 years ago by ▴ 740
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reply
697
views
can I use alignment utilities (mismatchTable, etc) on externally-generated alignments?
Alignment Cancer Alignment Cancer
updated 13.1 years ago by ★ 11k • written 13.1 years ago by ▴ 740
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views
Biostrings DNAMultipleAlignment vs AlignedXStringSet
Alignment convert Alignment convert
updated 13.3 years ago by 25k • written 13.3 years ago by ★ 13k
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ChIPpeakAnno - getAnnotation
Alignment Annotation Alignment Annotation
13.3 years ago Julie Zhu ★ 4.3k
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Package announcement: bsseq
Sequencing Alignment Cancer Colon bsseq Sequencing Alignment Cancer Colon bsseq
13.3 years ago Kasper Daniel Hansen ★ 6.5k
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Biostring: print sequence alignment to file
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 13.4 years ago by ▴ 100 • written 13.4 years ago by 16k
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obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array
Alignment probe Alignment probe
updated 13.4 years ago by 68k • written 13.4 years ago by ★ 1.0k
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GappedAlignmentPairs requests
Alignment Cancer GenomicRanges Alignment Cancer GenomicRanges
updated 13.4 years ago by ★ 11k • written 13.4 years ago by 16k
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Biostring: print sequence alignment to file
Sequencing Alignment Cancer Biostrings Sequencing Alignment Cancer Biostrings
updated 13.4 years ago by 16k • written 13.5 years ago by ▴ 100
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About Rsubread
Alignment Rsubread Alignment Rsubread
updated 13.5 years ago by ★ 3.6k • written 13.5 years ago by ★ 13k
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views
get genomic location
Alignment convert Alignment convert
updated 13.5 years ago by ★ 6.8k • written 13.5 years ago by ▴ 370
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pairwiseAlignment of PDB files to canonical protein structure
Alignment Biostrings PROcess Alignment Biostrings PROcess
13.5 years ago Gregory Ryslik ▴ 10
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reply
2.0k
views
Rsubread package usage and speed questions
Alignment Rsubread Alignment Rsubread
13.5 years ago Davis, Wade ▴ 350
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views
easyRNASeq Error in counting from C.elegans
Alignment Annotation Organism Alignment Annotation Organism
updated 13.5 years ago by ★ 1.2k • written 13.5 years ago by ▴ 40
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1.4k
views
miRNA and other small RNAs
miRNA Alignment Annotation PROcess miRNA Alignment Annotation PROcess
updated 13.5 years ago by ▴ 330 • written 13.5 years ago by ▴ 70
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views
Calculating alignment scores from aligned sequences
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 13.6 years ago by ★ 11k • written 13.6 years ago by ★ 13k
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6.9k
views
Biostring: print sequence alignment to file
Alignment Biostrings Alignment Biostrings
updated 13.6 years ago by ★ 1.7k • written 13.6 years ago by ▴ 100
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1.7k
views
DEXSeq error during fold change calculation
Alignment DEXSeq Alignment DEXSeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ★ 13k
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3
replies
1.8k
views
homopolymer gap extension penalty in Biostrings
Sequencing Alignment GO Cancer Sequencing Alignment GO Cancer
updated 13.7 years ago by ▴ 10 • written 13.7 years ago by 16k
0
votes
4
replies
2.1k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
13.8 years ago • updated 13.7 years ago delhomme@embl.de ★ 1.2k
0
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0
replies
943
views
IlluminaMousev2.db probe quality information questions?
Alignment Annotation probe convert Alignment Annotation probe convert
13.8 years ago Mark Dunning ★ 1.1k
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1
reply
2.5k
views
summarizeOverlaps vs countOverlaps
Alignment Alignment
updated 13.8 years ago by ★ 6.8k • written 13.8 years ago by ▴ 50
208 results • Page 3 of 5
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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