Showing : bsgenome • reset
0
votes
2
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1.2k
views
question about BSgenome and C.pombe genome, absent in USCS
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
updated 13.4 years ago by ▴ 30 • written 13.4 years ago by 16k
0
votes
1
reply
993
views
BSgenomes and protein sequences
BSgenome BSgenome BSgenome BSgenome
updated 13.5 years ago by ★ 6.8k • written 13.5 years ago by ▴ 30
0
votes
17
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3.5k
views
problems with strand in predictCoding
VariantAnnotation Annotation BSgenome BSgenome VariantAnnotation VariantAnnotation BSgenome
updated 13.5 years ago by ▴ 20 • written 13.5 years ago by ▴ 50
0
votes
2
replies
640
views
BSgenome.Celegans.UCSC.cd10 for WS220
BSgenome BSgenome BSgenome BSgenome
updated 13.5 years ago by 16k • written 13.5 years ago by ★ 4.3k
0
votes
3
replies
1.7k
views
Complementing alleles in a VCF
VariantAnnotation BSgenome BSgenome genomes VariantAnnotation VariantAnnotation BSgenome
updated 13.5 years ago by 25k • written 13.5 years ago by ▴ 650
0
votes
1
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1.3k
views
VariantAnnotation locateVariants - meaning of precedesID and followsID
BSgenome TranscriptDb BSgenome GenomicFeatures BSgenome TranscriptDb BSgenome
updated 13.5 years ago by ★ 6.8k • written 13.5 years ago by ▴ 80
0
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0
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791
views
question about BSgenome and C.pombe genome, absent in USCS
BSgenome BSgenome BSgenome BSgenome
13.5 years ago Zybaylov, Boris L ▴ 30
0
votes
2
replies
1.5k
views
Finding coding SNPs with predictCoding
SNP Annotation BSgenome ctc BSgenome cycle genomes SNP Annotation BSgenome ctc BSgenome
updated 13.5 years ago by ★ 1.7k • written 13.5 years ago by ★ 6.8k
0
votes
2
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1.3k
views
curious IRanges error when sort()ing a GRanges
GO BSgenome BSgenome GenomicRanges GO BSgenome BSgenome GenomicRanges
updated 13.6 years ago by 16k • written 13.6 years ago by ★ 4.2k
0
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0
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1.5k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO
13.6 years ago Matthew Young ▴ 50
0
votes
4
replies
2.1k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
13.6 years ago delhomme@embl.de ★ 1.2k
0
votes
4
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1.8k
views
Finding coding SNPs with predictCoding
SNP VariantAnnotation BSgenome SNPlocs BSgenome VariantAnnotation SNP VariantAnnotation
updated 13.6 years ago by ★ 6.8k • written 13.6 years ago by ▴ 650
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votes
0
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1.0k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings BSgenome rtracklayer goseq GO
13.6 years ago Alicia Oshlack ▴ 100
0
votes
0
replies
986
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer BSgenome Biostrings BSgenome rtracklayer GenomicFeatures goseq GO
13.6 years ago Hervé Pagès 16k
0
votes
0
replies
2.0k
views
Deferential gene expression databases
Microarray Genetics Annotation Normalization Pathways GO Cancer BSgenome probe annotate
13.7 years ago saikouy bah ▴ 30
0
votes
2
replies
1.9k
views
ChIPpeakAnno
GO BSgenome annotate BSgenome ChIPpeakAnno GO BSgenome annotate BSgenome ChIPpeakAnno
updated 13.7 years ago by ▴ 10 • written 13.7 years ago by ▴ 10
0
votes
13
replies
3.2k
views
How to plot NGS data?
GO BSgenome geneplotter PROcess BSgenome genomes GO BSgenome geneplotter PROcess genomes
updated 13.7 years ago by 25k • written 13.7 years ago by ▴ 30
0
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2
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2.2k
views
BSgenome installation error
BSgenome BSgenome BSgenome BSgenome
updated 13.7 years ago by 16k • written 13.7 years ago by ▴ 240
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votes
0
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1.3k
views
using easyRNASeq examples
RNASeq Annotation BSgenome convert biomaRt BSgenome IRanges DESeq easyRNASeq RNASeq
13.7 years ago delhomme@embl.de ★ 1.2k
0
votes
5
replies
1.8k
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
0
votes
0
replies
999
views
VariantAnnotation updated - error in predictCoding
BSgenome BSgenome BSgenome BSgenome
13.7 years ago Lescai, Francesco ▴ 380
0
votes
2
replies
1.2k
views
VariantAnnotation updated - error in predictCoding
BSgenome BSgenome BSgenome BSgenome
updated 13.7 years ago by ★ 6.8k • written 13.7 years ago by ▴ 380
0
votes
1
reply
1.2k
views
rtracklayer error
SNP BSgenome BSgenome rtracklayer SNP BSgenome BSgenome rtracklayer
updated 13.7 years ago by ★ 11k • written 13.7 years ago by ▴ 380
0
votes
1
reply
1.2k
views
intragenic sequence extraction
Annotation Cancer Organism BSgenome BSgenome GenomicFeatures Annotation Cancer Organism
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 90
0
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1
reply
1.3k
views
custom SNPlocs / BSgenome package
SNP Annotation Organism Homo sapiens BSgenome SNPlocs BSgenome SNP Annotation Organism
updated 13.9 years ago by 16k • written 13.9 years ago by ▴ 100
0
votes
1
reply
858
views
custom SNPlocs / BSgenome package
BSgenome BSgenome BSgenome BSgenome
updated 13.9 years ago by ★ 6.8k • written 13.9 years ago by ▴ 100
0
votes
1
reply
1.0k
views
Addition of Orangutan genome to BSgenomes
Genetics BSgenome BSgenome genomes Genetics BSgenome BSgenome genomes
updated 13.9 years ago by ★ 6.8k • written 13.9 years ago by ▴ 10
0
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0
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978
views
Fwd: extract introns
Cancer Organism BSgenome BSgenome Cancer Organism BSgenome BSgenome
13.9 years ago Steve Lianoglou ★ 13k
0
votes
3
replies
2.1k
views
Repitools/ClusterPlots
BSgenome BSgenome Repitools BSgenome BSgenome Repitools
updated 13.9 years ago by ▴ 580 • written 13.9 years ago by ★ 13k
0
votes
0
replies
1.1k
views
liftOver() issues
BSgenome BSgenome BSgenome BSgenome
14.0 years ago Tim Triche ★ 4.2k
0
votes
0
replies
817
views
BSgenome package for sacCer3
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
14.0 years ago Hervé Pagès 16k
0
votes
2
replies
1.9k
views
(BSgenome) forgeBSgenomeDataPkg for Sus scrofa problem
Sus scrofa BSgenome BSgenome Sus scrofa BSgenome BSgenome
updated 14.0 years ago by 16k • written 14.0 years ago by ▴ 160
0
votes
3
replies
1.9k
views
HowTo: "Extract masked sequences" / "insert Ns for repeat masked regions"
GO BSgenome BSgenome GO BSgenome BSgenome
updated 14.1 years ago by 16k • written 14.1 years ago by ★ 1.6k
0
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2
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2.6k
views
Biobase use problem
BSgenome BSgenome BSgenome BSgenome
updated 14.1 years ago by 21k • written 14.1 years ago by ▴ 30
0
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1
reply
1.0k
views
[Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2
Annotation GO BSgenome BSgenome ChIPpeakAnno Annotation GO BSgenome BSgenome ChIPpeakAnno
14.1 years ago Julie Zhu ★ 4.3k
0
votes
4
replies
2.1k
views
Extarcting large number of sequences using BSgenome package
BSgenome BSgenome BSgenome BSgenome
updated 14.2 years ago by 16k • written 14.2 years ago by ▴ 580
0
votes
5
replies
1.6k
views
Faster way to apply a function than endoapply on 40K GrangesList
BSgenome BSgenome BSgenome BSgenome
updated 14.2 years ago by 25k • written 14.2 years ago by ▴ 250
0
votes
1
reply
1.2k
views
Chippeakanno venn
GO BSgenome annotate BSgenome GO BSgenome annotate BSgenome
updated 14.2 years ago by ★ 4.3k • written 14.2 years ago by ▴ 90
0
votes
7
replies
2.4k
views
error in bayespeak function
ChIPSeq GO BSgenome BSgenome chipseq BayesPeak ChIPSeq GO BSgenome BSgenome chipseq
updated 14.2 years ago by ▴ 130 • written 14.2 years ago by ▴ 810
0
votes
0
replies
896
views
BSgenome package - danRer7 genome assembly
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
14.4 years ago Hervé Pagès 16k
0
votes
0
replies
677
views
BSgenome package - danRer7 genome assembly
BSgenome BSgenome BSgenome BSgenome
14.4 years ago Brett Maricque ▴ 10
0
votes
0
replies
1.5k
views
Using ChIPpeakAnno on a non-mainstream organism
Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno
14.5 years ago Julie Zhu ★ 4.3k
0
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0
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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
0
votes
2
replies
1.4k
views
How Does one subset a XStringView or PDict object?
Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome
updated 14.7 years ago by 25k • written 14.7 years ago by ▴ 410
0
votes
13
replies
3.4k
views
forge BSgenome data package
BSgenome Biostrings BSgenome BSgenome Biostrings BSgenome
updated 14.7 years ago by 16k • written 14.7 years ago by ▴ 330
0
votes
0
replies
631
views
BSgenome package for Stickleback
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
14.7 years ago Hervé Pagès 16k
0
votes
2
replies
1.9k
views
BSgenome package for a. thaliana
BSgenome BSgenome BSgenome BSgenome
updated 14.9 years ago by 16k • written 14.9 years ago by ▴ 20
0
votes
2
replies
1.2k
views
rtracklayer issues with other packages?
GO Cancer BSgenome graph Biostrings GOstats BSgenome rtracklayer GO Cancer BSgenome
updated 14.9 years ago by ★ 11k • written 14.9 years ago by ▴ 200
0
votes
1
reply
1.0k
views
Localizing repetitive regions on a chromosome
BSgenome biomaRt BSgenome rtracklayer BSgenome biomaRt BSgenome rtracklayer
updated 14.9 years ago by ★ 11k • written 14.9 years ago by ▴ 500
0
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3
replies
1.3k
views
rtracklayer -- how to hide some default tracks? fine-grained control of track view mode (pack, full, dense, squish...)
BSgenome BSgenome BSgenome BSgenome
updated 15.0 years ago by ★ 11k • written 15.0 years ago by ★ 1.1k
349 results • Page 6 of 7
Recent ...
Replies
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…
Votes
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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