Showing : bsgenome • reset
0
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2
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1.2k
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BSgenome.Dmelanogaster.UCSC.dm3 package for R 3.0.0 beta?
BSgenome BSgenome BSgenome BSgenome
updated 12.6 years ago by 68k • written 12.6 years ago by ▴ 340
0
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5
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10k
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how to operate on a DNAStringSet object
BSgenome BSgenome BSgenome BSgenome
12.6 years ago Chris Seidel ▴ 80
0
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2
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2.8k
views
MT reference differences between hg19/GRCH37
BSgenome BSgenome BSgenome BSgenome
12.6 years ago Julian Gehring ★ 1.3k
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5
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2.6k
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yieldSize and paired end data in SummarizeOverlaps error?
BSgenome PROcess BSgenome ASSIGN BSgenome PROcess BSgenome ASSIGN
updated 12.6 years ago by ★ 6.8k • written 12.6 years ago by ▴ 10
0
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1
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1.6k
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Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 12.6 years ago by ▴ 570 • written 12.6 years ago by ▴ 290
0
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1
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2.9k
views
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") fails
BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC
updated 12.6 years ago by ★ 8.2k • written 12.6 years ago by ▴ 100
0
votes
4
replies
2.1k
views
IlluminaHumanMethylation450kprobe for nearest TSS calculation question
Annotation BSgenome SNPlocs BSgenome Annotation BSgenome SNPlocs BSgenome
updated 12.6 years ago by ★ 4.2k • written 12.6 years ago by ★ 13k
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0
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1.0k
views
BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
GUI BSgenome BSgenome GUI BSgenome BSgenome
12.6 years ago Dan Tenenbaum ★ 8.2k
0
votes
2
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1.4k
views
Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray Preprocessing BSgenome BSgenome MEDIPS Microarray Preprocessing BSgenome MEDIPS
updated 12.7 years ago by ▴ 290 • written 12.7 years ago by ▴ 570
0
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0
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950
views
CHARM: Affymetrix 1.0R tiling arrays import
BSgenome affy BSgenome oligo charm BSgenome affy BSgenome oligo charm
12.7 years ago Guest User ★ 13k
0
votes
2
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839
views
adding papaya genome to BSgenome
BSgenome BSgenome BSgenome BSgenome
updated 12.7 years ago by 16k • written 12.7 years ago by ★ 13k
0
votes
0
replies
945
views
Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray BSgenome BSgenome MEDIPS Microarray BSgenome BSgenome MEDIPS
12.7 years ago Stephen Turner ▴ 290
0
votes
3
replies
1.1k
views
curious behavior from VariantAnnotation 1.5.36
GO BSgenome BSgenome GO BSgenome BSgenome
12.7 years ago Tim Triche ★ 4.2k
0
votes
3
replies
1.4k
views
DiffBind - Scores for peakset are all the same
GO BSgenome BSgenome GO BSgenome BSgenome
updated 12.7 years ago by ★ 5.2k • written 12.7 years ago by ▴ 510
0
votes
1
reply
833
views
rtracklayer weirdness
BSgenome BSgenome rtracklayer BSgenome BSgenome rtracklayer
updated 12.7 years ago by ★ 11k • written 12.7 years ago by ★ 4.2k
0
votes
0
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1.0k
views
Error - BSgenomeForge function
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
12.7 years ago Hervé Pagès 16k
0
votes
2
replies
1.6k
views
BSgenome forging - Node stack overflow
BSgenome BSgenome BSgenome BSgenome
updated 12.7 years ago by 16k • written 12.7 years ago by ▴ 40
0
votes
2
replies
1.2k
views
rtracklayer: small problem
BSgenome BSgenome rtracklayer BSgenome BSgenome rtracklayer
updated 12.7 years ago by ★ 11k • written 12.7 years ago by ▴ 440
0
votes
3
replies
3.1k
views
seqlevels in VCF objects
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 12.8 years ago by ★ 6.8k • written 12.8 years ago by ▴ 70
0
votes
1
reply
1.6k
views
easyRNAseq remove overlapping features
Annotation BSgenome BSgenome IRanges easyRNASeq Annotation BSgenome BSgenome IRanges
updated 12.8 years ago by ★ 1.2k • written 12.8 years ago by ▴ 160
0
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0
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785
views
Bos taurus genome
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
12.8 years ago Hervé Pagès 16k
0
votes
1
reply
902
views
Empty Granges
BSgenome BSgenome BSgenome BSgenome
updated 12.8 years ago by ★ 6.8k • written 12.8 years ago by ▴ 10
0
votes
0
replies
1.9k
views
Error message with transcriptCounts(easyRNASeq) performed with gtf file generated with cuffmerge
RNASeq Annotation Normalization Cancer Organism BSgenome BSgenome easyRNASeq RNASeq
12.8 years ago Richard Friedman ★ 2.0k
0
votes
8
replies
2.8k
views
vmatchPDict?
BSgenome probe BSgenome BSgenome probe BSgenome
updated 12.8 years ago by 16k • written 12.8 years ago by ▴ 130
0
votes
0
replies
831
views
discrepancy between gene models in easyRNASeq and provided exon annotation
RNASeq Annotation Organism BSgenome BSgenome RNASeq Annotation Organism BSgenome BSgenome
12.9 years ago Guest User ★ 13k
0
votes
1
reply
1.2k
views
easyRNASeq and edgeR
BSgenome BSgenome edgeR easyRNASeq BSgenome BSgenome edgeR easyRNASeq
updated 12.9 years ago by ★ 1.2k • written 12.9 years ago by ★ 13k
0
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1
reply
1.5k
views
repeat mask for mm10?
BSgenome BSgenome BSgenome BSgenome
12.9 years ago Janet Young ▴ 740
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1
reply
1.6k
views
error in easyRNASeq
RNASeq BSgenome BSgenome easyRNASeq RNASeq BSgenome BSgenome easyRNASeq
updated 12.9 years ago by ★ 1.2k • written 12.9 years ago by ▴ 510
4
votes
2
replies
3.5k
views
How to get sequences corresponding to a GRanges?
BSgenome BSgenome BSgenome BSgenome
updated 13.0 years ago by 25k • written 13.0 years ago by ▴ 830
0
votes
1
reply
783
views
rtracklayer 1.18 vignette bug in track()
BSgenome BSgenome BSgenome BSgenome
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ▴ 10
0
votes
4
replies
2.5k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 13.0 years ago by 16k • written 13.0 years ago by ▴ 100
0
votes
3
replies
1.7k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 13.0 years ago by 16k • written 13.0 years ago by ▴ 100
0
votes
6
replies
2.7k
views
chromosome name match among vcf, txdb,BSgenome
Annotation BSgenome BSgenome Annotation BSgenome BSgenome
updated 13.0 years ago by 16k • written 13.0 years ago by ▴ 100
0
votes
2
replies
1.9k
views
Building custom genome in MeDIPS
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 13.1 years ago by 68k • written 13.1 years ago by ▴ 10
0
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2
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887
views
Fetch scaffold sequences from BSgenome package
BSgenome BSgenome BSgenome BSgenome
updated 13.1 years ago by 16k • written 13.1 years ago by ★ 4.3k
0
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2
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1.4k
views
easyRNASeq package: error when summarizing per gene
RNASeq Annotation Organism BSgenome BSgenome easyRNASeq RNASeq Annotation Organism
updated 13.1 years ago by ★ 1.2k • written 13.1 years ago by ★ 13k
0
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1
reply
1.2k
views
How to use cutome reference genome?
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 13.1 years ago by ★ 6.5k • written 13.1 years ago by ★ 13k
0
votes
1
reply
2.3k
views
ChipPeakAnno / GRanges isolate peaks that do NOT overlap
GO GUI BSgenome BSgenome GO GUI BSgenome BSgenome
updated 13.1 years ago by ★ 4.3k • written 13.1 years ago by ▴ 110
0
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13
replies
2.4k
views
Where to get BAM files for easyRNASeq human use case
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
updated 13.2 years ago by ★ 1.2k • written 13.2 years ago by ★ 2.0k
0
votes
0
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1.2k
views
ChIPpeakAnno to find peaks nearest to miRNA
miRNA Annotation GO BSgenome biomaRt BSgenome ChIPpeakAnno miRNA Annotation GO BSgenome
13.2 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
605
views
Request to add the latest dog genome release to BSGenome
BSgenome BSgenome BSgenome BSgenome
updated 13.2 years ago by 16k • written 13.2 years ago by ▴ 10
0
votes
3
replies
2.2k
views
ChIPpeakAnno to find peaks nearest to miRNA
miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno
updated 13.2 years ago by ★ 4.3k • written 13.2 years ago by ▴ 350
0
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0
replies
1.1k
views
ChIPpeakAnno - Annotation of miRNA
miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno
13.2 years ago Paolo Kunderfranco ▴ 350
0
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1
reply
1.5k
views
Warnings with running easyRNASeq with easyRNASeq tutorial
RNASeq Annotation GUI Cancer BSgenome BSgenome easyRNASeq RNASeq Annotation GUI Cancer
updated 13.2 years ago by ★ 1.2k • written 13.2 years ago by ★ 2.0k
0
votes
0
replies
1.1k
views
reads of different lengths (easyRNASeq)
Annotation Organism BSgenome convert BSgenome easyRNASeq Annotation Organism BSgenome
13.3 years ago delhomme@embl.de ★ 1.2k
0
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4
replies
1.1k
views
BSgenome packages for new UCSC rn5 and galGal4 assemblies
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
updated 13.3 years ago by ★ 6.5k • written 13.3 years ago by 16k
0
votes
1
reply
970
views
RnaSeqTutorial Package
Annotation BSgenome BSgenome DESeq DEXSeq Annotation BSgenome BSgenome DESeq DEXSeq
updated 13.3 years ago by ★ 13k • written 13.3 years ago by ★ 13k
0
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1
reply
3.8k
views
GRanges Constructor With seqlengths
BSgenome BSgenome BSgenome BSgenome
13.4 years ago Dario Strbenac ★ 1.6k
0
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1
reply
1.1k
views
Finding coding SNPs with predictCoding
SNP Annotation BSgenome BSgenome GenomicFeatures cycle genomes SNP Annotation BSgenome
updated 13.4 years ago by ★ 1.7k • written 13.4 years ago by ★ 6.8k
0
votes
1
reply
866
views
BSgenome packages for ce10 and panTro3 (was Re: BSgenome.Celegans.UCSC.cd10 for WS220)
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
updated 13.4 years ago by ★ 4.3k • written 13.4 years ago by 16k
349 results • Page 5 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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