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 12.2 years ago by ▴ 570 • written 12.2 years ago by ▴ 40
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job advertisement
Genetics Alignment Visualization Genetics Alignment Visualization
12.2 years ago Zhenyu Xu ▴ 10
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5
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2.4k
views
filterBam
Alignment Alignment
updated 12.2 years ago by ▴ 500 • written 12.2 years ago by ▴ 500
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ReportingTools: formatting html report
Alignment ReportingTools Alignment ReportingTools
12.3 years ago Gabriel Becker ▴ 70
2
votes
5
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1.7k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment GO Cancer BSgenome BSgenome Alignment GO Cancer BSgenome BSgenome
updated 12.3 years ago by 25k • written 12.3 years ago by ★ 13k
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3
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2.8k
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DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 12.4 years ago by 43k • written 12.4 years ago by ▴ 150
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4
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2.0k
views
Howto annotate blast subject.id with AnnotationDbi
Alignment GO annotate AnnotationDbi Alignment GO annotate AnnotationDbi
updated 12.4 years ago by ★ 7.2k • written 12.4 years ago by ▴ 40
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1
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2.0k
views
DEXSeq Problems
Alignment Homo sapiens PROcess Alignment Homo sapiens PROcess
updated 12.4 years ago by ★ 3.8k • written 12.4 years ago by ▴ 150
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3
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2.2k
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multiple feature/mode counting with summarizeOverlaps
Alignment Alignment
12.4 years ago Thomas Girke ★ 1.7k
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2
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1.5k
views
tutorials for RNA-seq analysis in Bioconductor
Alignment Alignment
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ▴ 70
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2
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2.0k
views
QuasR special case alignment
Alignment genomes QuasR Alignment genomes QuasR
updated 12.4 years ago by ▴ 340 • written 12.4 years ago by ▴ 350
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3
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1.4k
views
Deleting object rows while looping - II
Coverage Alignment Cancer PROcess Coverage Alignment Cancer PROcess
updated 12.4 years ago by ★ 13k • written 12.4 years ago by 16k
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3
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1.8k
views
Deleting object rows while looping - II
Coverage Alignment PROcess Coverage Alignment PROcess
updated 12.4 years ago by 25k • written 12.4 years ago by ▴ 90
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2
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1.6k
views
QuasR special case alignment
Alignment QuasR Alignment QuasR
updated 12.5 years ago by ▴ 350 • written 12.5 years ago by ▴ 340
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vote
1
reply
2.4k
views
multiple threads on QuasR
Alignment GLAD QuasR Alignment GLAD QuasR
12.5 years ago Michael Stadler ▴ 350
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1
reply
1.2k
views
loss of stranding in alignments from recent versions of Rsubread
Alignment Alignment
updated 12.5 years ago by ★ 3.6k • written 12.5 years ago by ★ 4.2k
0
votes
7
replies
2.1k
views
MEDIPS error extending reads
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 12.5 years ago by ▴ 570 • written 12.5 years ago by ▴ 290
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2
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1.6k
views
BitSeq transcript IDs
Alignment PROcess BitSeq Alignment PROcess BitSeq
updated 12.5 years ago by ▴ 30 • written 12.5 years ago by ▴ 70
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1
reply
1.4k
views
MEDIPS
Sequencing Alignment MEDIPS Sequencing Alignment MEDIPS
updated 12.5 years ago by ▴ 570 • written 12.5 years ago by ▴ 350
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votes
1
reply
1.4k
views
BitSeq getExpression crash
Alignment PROcess BitSeq Alignment PROcess BitSeq
updated 12.5 years ago by ▴ 70 • written 12.5 years ago by ▴ 30
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5
replies
2.1k
views
Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 12.6 years ago by ▴ 420 • written 12.6 years ago by ★ 11k
1
vote
5
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5.4k
views
DiffBind error
Alignment DiffBind Alignment DiffBind
updated 12.7 years ago by ★ 5.2k • written 12.7 years ago by ▴ 280
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votes
21
replies
8.2k
views
BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 22 months ago by • 0 • written 12.8 years ago by ▴ 280
0
votes
1
reply
1.8k
views
Minimal input data format for bsseq
Sequencing Alignment bsseq Sequencing Alignment bsseq
updated 12.8 years ago by ★ 6.5k • written 12.8 years ago by ▴ 20
0
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2
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1.6k
views
EdgeR estimateTagwiseDisp()
Alignment edgeR Alignment edgeR
updated 12.8 years ago by 53k • written 12.8 years ago by ★ 13k
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0
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998
views
readAligned with bowtie2 input
Alignment Cancer ShortRead Alignment Cancer ShortRead
12.9 years ago Martin Morgan 25k
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0
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986
views
readAligned with bowtie2 input
Alignment ShortRead Alignment ShortRead
12.9 years ago Maria Dermit ▴ 10
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0
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1.5k
views
get synthetic exon dataset with easyRNASeq
RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO
12.9 years ago delhomme@embl.de ★ 1.2k
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1
reply
896
views
bug in Biostrings mismatchTable?
Alignment Alignment
updated 13.0 years ago by 16k • written 13.0 years ago by ▴ 740
0
votes
1
reply
670
views
can I use alignment utilities (mismatchTable, etc) on externally-generated alignments?
Alignment Cancer Alignment Cancer
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ▴ 740
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1
reply
2.4k
views
Biostrings DNAMultipleAlignment vs AlignedXStringSet
Alignment convert Alignment convert
updated 13.1 years ago by 25k • written 13.1 years ago by ★ 13k
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0
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1.4k
views
ChIPpeakAnno - getAnnotation
Alignment Annotation Alignment Annotation
13.1 years ago Julie Zhu ★ 4.3k
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1.7k
views
Package announcement: bsseq
Sequencing Alignment Cancer Colon bsseq Sequencing Alignment Cancer Colon bsseq
13.2 years ago Kasper Daniel Hansen ★ 6.5k
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6
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2.5k
views
Biostring: print sequence alignment to file
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 13.2 years ago by ▴ 100 • written 13.2 years ago by 16k
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7
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3.0k
views
obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array
Alignment probe Alignment probe
updated 13.2 years ago by 68k • written 13.2 years ago by ★ 1.0k
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5
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1.4k
views
GappedAlignmentPairs requests
Alignment Cancer GenomicRanges Alignment Cancer GenomicRanges
updated 13.3 years ago by ★ 11k • written 13.3 years ago by 16k
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1
reply
1.0k
views
Biostring: print sequence alignment to file
Sequencing Alignment Cancer Biostrings Sequencing Alignment Cancer Biostrings
updated 13.3 years ago by 16k • written 13.3 years ago by ▴ 100
0
votes
1
reply
1.2k
views
About Rsubread
Alignment Rsubread Alignment Rsubread
updated 13.3 years ago by ★ 3.6k • written 13.3 years ago by ★ 13k
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2
replies
2.0k
views
get genomic location
Alignment convert Alignment convert
updated 13.3 years ago by ★ 6.8k • written 13.3 years ago by ▴ 370
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votes
0
replies
1000
views
pairwiseAlignment of PDB files to canonical protein structure
Alignment Biostrings PROcess Alignment Biostrings PROcess
13.4 years ago Gregory Ryslik ▴ 10
0
votes
1
reply
1.9k
views
Rsubread package usage and speed questions
Alignment Rsubread Alignment Rsubread
13.4 years ago Davis, Wade ▴ 350
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votes
2
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1.4k
views
easyRNASeq Error in counting from C.elegans
Alignment Annotation Organism Alignment Annotation Organism
updated 13.4 years ago by ★ 1.2k • written 13.4 years ago by ▴ 40
0
votes
1
reply
1.3k
views
miRNA and other small RNAs
miRNA Alignment Annotation PROcess miRNA Alignment Annotation PROcess
updated 13.4 years ago by ▴ 330 • written 13.4 years ago by ▴ 70
0
votes
2
replies
1.9k
views
Calculating alignment scores from aligned sequences
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ★ 13k
0
votes
11
replies
6.7k
views
Biostring: print sequence alignment to file
Alignment Biostrings Alignment Biostrings
updated 13.5 years ago by ★ 1.7k • written 13.5 years ago by ▴ 100
0
votes
2
replies
1.7k
views
DEXSeq error during fold change calculation
Alignment DEXSeq Alignment DEXSeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ★ 13k
0
votes
3
replies
1.8k
views
homopolymer gap extension penalty in Biostrings
Sequencing Alignment GO Cancer Sequencing Alignment GO Cancer
updated 13.6 years ago by ▴ 10 • written 13.6 years ago by 16k
0
votes
4
replies
2.0k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
13.6 years ago delhomme@embl.de ★ 1.2k
0
votes
0
replies
919
views
IlluminaMousev2.db probe quality information questions?
Alignment Annotation probe convert Alignment Annotation probe convert
13.6 years ago Mark Dunning ★ 1.1k
0
votes
1
reply
2.4k
views
summarizeOverlaps vs countOverlaps
Alignment Alignment
updated 13.6 years ago by ★ 6.8k • written 13.6 years ago by ▴ 50
208 results • Page 3 of 5
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
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Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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