Showing : alignment • reset
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summarizeOverlaps vs countOverlaps
Alignment Alignment
updated 13.6 years ago by ★ 6.8k • written 13.6 years ago by ▴ 50
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Biostrings - pairwiseAlignment trimmed pattern returned
Alignment Biostrings Alignment Biostrings
updated 13.6 years ago by ★ 6.8k • written 13.7 years ago by ▴ 210
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5
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views
easyRNASeq - error reading single chromosome bam
RNASeq Alignment BSgenome BSgenome RNASeq Alignment BSgenome BSgenome
updated 13.7 years ago by ★ 1.2k • written 13.7 years ago by ▴ 380
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1.1k
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rtrackplayer UCSC multiz maf download
Alignment Alignment
updated 13.7 years ago by ★ 11k • written 13.7 years ago by ★ 13k
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7
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2.6k
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about reduce function in GenomicRanges
Alignment Alignment
13.7 years ago Tarca, Adi ▴ 570
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2
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1.3k
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pairwise alignment and homology score
Alignment Alignment
updated 13.8 years ago by 16k • written 13.8 years ago by ▴ 10
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Fwd: the diffrent alignment result between pairwiseAlignment() in Biostrings package and EBI-webserver
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 13.8 years ago by ★ 6.8k • written 13.8 years ago by ▴ 50
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the diffrent alignment result between pairwiseAlignment() in Biostrings package and EBI-webserver
Alignment Biostrings Alignment Biostrings
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 50
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Reading paired-end data into GRangesList
Alignment Alignment
updated 14.0 years ago by ▴ 970 • written 14.0 years ago by ▴ 100
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1
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1.2k
views
Regarding subread vignette
Sequencing Alignment Rsubread Sequencing Alignment Rsubread
14.0 years ago Wei Shi ★ 3.6k
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995
views
align microRNA with custom mRNA sequences
Alignment Cancer Biostrings microRNA Alignment Cancer Biostrings microRNA
14.2 years ago Hervé Pagès 16k
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1.5k
views
occurrence of rGADEM motifs (mattia pelizzola)
Alignment rGADEM MotIV Alignment rGADEM MotIV
14.2 years ago Mercier Eloi ▴ 60
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1.3k
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occurrence of rGADEM motifs (mattia pelizzola)
Alignment rGADEM MotIV Alignment rGADEM MotIV
14.2 years ago Chris Whelan ▴ 60
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8
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2.6k
views
Rsubread alingner
Alignment Yeast Rsubread Alignment Yeast Rsubread
14.5 years ago Wei Shi ★ 3.6k
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1.2k
views
Whole genome searching of 100bp "D" sequence
Alignment BSgenome BSgenome Alignment BSgenome BSgenome
14.5 years ago Amos Folarin ▴ 80
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1.1k
views
[Course] CSAMA 2011: Computational Statistics for Genome Biology (Ninth Edition)
Sequencing Microarray Alignment Annotation Clustering Cancer Biostrings AnnotationDbi
14.5 years ago stefano iacus ▴ 430
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1
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1.1k
views
pairwiseAlignment generates different outcomes for the same inp...
Alignment Cancer probe Alignment Cancer probe
updated 14.6 years ago by 16k • written 14.6 years ago by ▴ 90
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1
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1.7k
views
Help about 'pairwiseAlignment' in Biostrings package
Alignment Biostrings Alignment Biostrings
updated 14.6 years ago by 16k • written 14.6 years ago by ▴ 450
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9
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2.4k
views
Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 14.6 years ago by 21k • written 14.6 years ago by 16k
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3
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views
Mapping microarray probes to the genome using findOverlaps
Alignment Annotation zebrafish probe Alignment Annotation zebrafish probe
updated 14.6 years ago by 21k • written 14.6 years ago by ▴ 140
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1
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1.8k
views
Cell DNA content data normalization and gating
Alignment flowCore Alignment flowCore
updated 14.6 years ago by ▴ 240 • written 14.6 years ago by ▴ 10
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0
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1.2k
views
How do I use biomaRt to get upstreamFlank Genomic Sequence for many Genomes?
Alignment biomaRt genomes Alignment biomaRt genomes
14.8 years ago Noah Dowell ▴ 410
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1
reply
1.2k
views
missing reads in alignerBAM
Alignment convert Alignment convert
updated 14.8 years ago by 25k • written 14.8 years ago by ▴ 90
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2
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2.8k
views
alignment & SNP calling
Alignment Alignment
updated 14.9 years ago by ▴ 810 • written 14.9 years ago by ▴ 90
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1
reply
1.3k
views
ShortRead qa() for BAM files?
Coverage Alignment ShortRead Coverage Alignment ShortRead
updated 15.0 years ago by 25k • written 15.0 years ago by ▴ 260
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5
replies
2.7k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment Biostrings Alignment Biostrings
15.3 years ago Coghlan, Avril ▴ 190
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1
reply
1.1k
views
get table with aanotaed genome features
Alignment annotate girafe Alignment annotate girafe
updated 15.3 years ago by ▴ 450 • written 15.3 years ago by ▴ 810
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2
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views
using Blat in R
Alignment PROcess Alignment PROcess
updated 15.5 years ago by ★ 1.9k • written 15.5 years ago by ▴ 250
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2
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views
chip-seq data analysis
Transcription ChIPSeq Alignment chipseq Transcription ChIPSeq Alignment chipseq
updated 15.6 years ago by 21k • written 15.6 years ago by ▴ 60
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1.0k
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Mapping using absolute coordinates
Alignment Alignment
15.6 years ago Ludo Pagie ▴ 20
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1
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901
views
affyBatch: probes from intensity table not listed in the output of indexProbes()
Alignment affy Alignment affy
updated 15.7 years ago by ▴ 30 • written 15.7 years ago by 68k
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1.3k
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unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment Alignment
15.7 years ago Patrick Aboyoun ★ 1.6k
2
votes
0
replies
1.2k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment Alignment
15.7 years ago Coghlan, Avril ▴ 190
0
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1
reply
1.0k
views
ShortRead - readAligned() with bowtie & qual
Alignment Alignment
updated 15.7 years ago by ★ 6.5k • written 15.7 years ago by ▴ 100
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0
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1.7k
views
unexpected genes names list using getBM{biomaRt}
Alignment convert biomaRt Alignment convert biomaRt
15.8 years ago steffen@stat.Berkeley.EDU ▴ 600
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854
views
clustalW
Alignment Alignment
15.9 years ago Coghlan, Avril ▴ 190
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votes
1
reply
987
views
possible bug in extendReads() in package chipseq
Alignment ShortRead Alignment ShortRead
updated 15.9 years ago by 25k • written 15.9 years ago by ▴ 40
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0
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views
suggested Biostrings library function for printing an alignment
Alignment Biostrings Alignment Biostrings
15.9 years ago Coghlan, Avril ▴ 190
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2
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1.4k
views
pileup function in ShortRead package
Alignment ShortRead Alignment ShortRead
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 40
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1
reply
2.0k
views
getSequence: difference between coding_gene_flank and 5utr
Alignment Alignment
updated 16.0 years ago by ▴ 660 • written 16.0 years ago by ▴ 220
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0
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1.2k
views
R: Pairwise Sequence Alignments
miRNA Alignment biomaRt miRNA Alignment biomaRt
16.2 years ago mauede@alice.it ▴ 870
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1
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1.0k
views
Pairwise Sequence Alignments
Alignment Alignment
updated 16.2 years ago by 21k • written 16.2 years ago by ▴ 870
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2
replies
1.3k
views
scoring matrices
Alignment Alignment
updated 16.2 years ago by ▴ 190 • written 16.2 years ago by ▴ 870
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0
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1.1k
views
visualization and alignment of affymetirx probe sequence to transcripts
Alignment probe Alignment probe
16.6 years ago shirley zhang ★ 1.0k
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0
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875
views
visualization and alignment of affymetirx probe sequence to transcripts
Alignment probe Alignment probe
16.6 years ago shirley zhang ★ 1.0k
0
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8
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2.0k
views
memory exhausted for readAligned
Alignment Alignment
updated 16.7 years ago by 25k • written 16.7 years ago by ★ 1.3k
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3
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1.9k
views
Genome position to miRNA or gene name
miRNA Alignment GO Cancer BSgenome BSgenome miRNA Alignment GO Cancer BSgenome BSgenome
updated 16.7 years ago by 25k • written 16.7 years ago by ★ 1.9k
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0
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1.4k
views
SAM warning
Biophysics Alignment Annotation Normalization Cancer hgu133plus2 probe affy vsn MBCB vsn
16.7 years ago elliot harrison ▴ 230
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0
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1.1k
views
multiple locations for probeset in hgu133plus2CHRLOC vs. UCSC PSL data
Alignment Annotation Cancer hgu133plus2 probe affy Biostrings Alignment Annotation Cancer
16.7 years ago rgentleman ★ 5.5k
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votes
5
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1.8k
views
multiple locations for probeset in hgu133plus2CHRLOC vs. UCSC PSL data
Alignment Annotation hgu133plus2 Alignment Annotation hgu133plus2
updated 16.9 years ago by 16k • written 16.9 years ago by ▴ 10
208 results • Page 4 of 5
Recent ...
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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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