Showing : Iranges • reset
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working with genome-wide phastCons scores
BSgenome convert BSgenome rtracklayer IRanges charm BSgenome convert BSgenome rtracklayer
12.0 years ago Robert Castelo ★ 3.4k
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2
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7.2k
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how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 12.0 years ago by ★ 11k • written 12.0 years ago by 16k
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4
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2.4k
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Getting first or last hit from a Hits object
IRanges GenomicRanges IRanges GenomicRanges
updated 12.0 years ago by ★ 11k • written 12.0 years ago by ▴ 760
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2
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Fwd: BioStrings PairwiseAlignment deletion() insertion() function
Alignment Cancer Biostrings IRanges Alignment Cancer Biostrings IRanges
updated 12.0 years ago by ▴ 30 • written 12.0 years ago by 16k
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1.4k
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'version' is missing error when running makeTxDbPackageFromUCSC
TranscriptDb IRanges TranscriptDb IRanges
updated 12.1 years ago by ★ 8.2k • written 12.1 years ago by ▴ 40
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Course: Understanding R / Bioconductor, Sept 30-Oct 1, Seattle
Cancer Biostrings biomaRt IRanges GenomicRanges Cancer Biostrings biomaRt IRanges
12.1 years ago Martin Morgan 25k
0
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3
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3.3k
views
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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1.4k
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*Ranges paper published
Infrastructure IRanges GenomicFeatures GenomicRanges Infrastructure IRanges GenomicFeatures
updated 12.2 years ago by ★ 4.2k • written 12.2 years ago by ★ 11k
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4
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1.7k
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IRanges::unlist in package
rtracklayer IRanges GenomicFeatures Rsamtools rtracklayer IRanges GenomicFeatures Rsamtools
updated 12.2 years ago by 68k • written 12.2 years ago by ▴ 220
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16
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2.3k
views
IRanges is broken in Cygwin (mingw/math.h)
IRanges IRanges
updated 12.3 years ago by ★ 11k • written 12.3 years ago by ▴ 680
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2
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1.3k
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transport mcols from one GRange obejct to another
IRanges IRanges
updated 12.5 years ago by 25k • written 12.5 years ago by ▴ 100
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1
reply
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
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3
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1.2k
views
startup options
IRanges IRanges
updated 12.6 years ago by ★ 4.3k • written 12.6 years ago by ★ 6.5k
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0
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807
views
Expected value of finding a sequence
Biostrings IRanges Biostrings IRanges
12.6 years ago Tim Smith ★ 1.1k
1
vote
0
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2.1k
views
pileup coverage from BAM file
Coverage Cancer IRanges GenomicRanges Coverage Cancer IRanges GenomicRanges
12.6 years ago Martin Morgan 25k
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0
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1.0k
views
question about how to get ranges in Biostrings
Cancer IRanges Gviz Cancer IRanges Gviz
12.6 years ago Hervé Pagès 16k
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2
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4.0k
views
Generate a GRangesList from a classical list of GRangesObjects
IRanges IRanges
updated 12.6 years ago by ★ 4.2k • written 12.6 years ago by ▴ 170
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0
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978
views
Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
GO IRanges GO IRanges
12.7 years ago Stephanie M. Gogarten ▴ 890
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4
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2.1k
views
Using GenomicRanges with table data
IRanges GenomicRanges IRanges GenomicRanges
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 60
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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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28
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3.8k
views
countMatches() (was: table for GenomicRanges)
Cancer IRanges Cancer IRanges
updated 12.8 years ago by ★ 11k • written 12.8 years ago by 16k
0
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1
reply
1.3k
views
IRanges install error with parallel/mcmapply
Coverage IRanges Coverage IRanges
updated 12.9 years ago by ★ 8.2k • written 12.9 years ago by ▴ 10
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8
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2.5k
views
IRanges/List oddity: do.call of `c` on a list of IRangesList returns "list" only when the list is named
Cancer IRanges BiocGenerics Cancer IRanges BiocGenerics
updated 12.9 years ago by ★ 11k • written 12.9 years ago by 16k
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0
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809
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[Bioc-devel] knowing what is changed/new in release patches
IRanges IRanges
12.9 years ago Malcolm Cook ★ 1.6k
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1.6k
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Rle factors, table and empty levels
IRanges IRanges
12.9 years ago Valerie Obenchain ★ 6.8k
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4
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960
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knowing what is changed/new in release patches
IRanges IRanges
updated 12.9 years ago by ★ 6.5k • written 12.9 years ago by ★ 1.6k
0
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1
reply
2.3k
views
compilation failed for package \'IRanges\' @str_utils.c(152) identifier \"timezone\" is undefined
Coverage IRanges Coverage IRanges
updated 12.9 years ago by ★ 8.2k • written 12.9 years ago by ★ 13k
0
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1
reply
686
views
Rle factors, table and empty levels
IRanges IRanges
updated 13.0 years ago by ★ 6.8k • written 13.0 years ago by ▴ 20
0
votes
1
reply
2.9k
views
Integer overflow when summing an 'integer' Rle
Coverage GO Cancer convert IRanges Coverage GO Cancer convert IRanges
updated 13.1 years ago by ★ 1.2k • written 13.1 years ago by ★ 6.8k
0
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0
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1.6k
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GenomicRanges: nearest() for GRanges not returning overlaps
IRanges GenomicRanges IRanges GenomicRanges
13.1 years ago Valerie Obenchain ★ 6.8k
0
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1
reply
1.1k
views
nearest for GRanges ignoring overlapping ranges
Cancer IRanges GenomicRanges Cancer IRanges GenomicRanges
updated 13.1 years ago by ★ 6.8k • written 13.1 years ago by ▴ 740
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2
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1.3k
views
distanceToNearest for GRanges?
IRanges GenomicRanges IRanges GenomicRanges
updated 13.1 years ago by ★ 6.8k • written 13.1 years ago by ▴ 740
0
votes
8
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2.4k
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good news and bad news
Infrastructure Cancer IRanges GenomicRanges Infrastructure Cancer IRanges GenomicRanges
updated 13.2 years ago by ★ 13k • written 13.2 years ago by 16k
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4
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3.0k
views
error in exomeCopy - IRanges?
IRanges exomeCopy IRanges exomeCopy
updated 13.2 years ago by ▴ 150 • written 13.2 years ago by ▴ 380
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8
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2.2k
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IRanges problem: findOverlaps
IRanges IRanges
updated 13.3 years ago by ▴ 50 • written 13.3 years ago by ▴ 20
0
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6
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2.0k
views
IRanges coverage integer limit?
Coverage IRanges Coverage IRanges
updated 13.3 years ago by 16k • written 13.3 years ago by ★ 1.2k
0
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5
replies
1.9k
views
GenomicRanges: nearest() for GRanges not returning overlaps
IRanges IRanges
updated 13.3 years ago by ★ 11k • written 13.3 years ago by ▴ 300
0
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4
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1.0k
views
Getting the length of every element from a large CompressedIRangesList is slow
IRanges IRanges
13.3 years ago delhomme@embl.de ★ 1.2k
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11
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2.6k
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nearest() for GRanges
IRanges IRanges
updated 13.3 years ago by 25k • written 13.3 years ago by ▴ 20
0
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1
reply
1.7k
views
FW: Overlay Gene Expression on SNP (copy number) data
SNP Coverage Network Cancer TranscriptDb IRanges RCytoscape ggbio Gviz SNP Coverage
updated 13.5 years ago by ★ 4.2k • written 13.5 years ago by ▴ 370
0
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1
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1.2k
views
seqbias : how to correct weight of mapped short reads?
Coverage IRanges seqbias Coverage IRanges seqbias
updated 13.5 years ago by 25k • written 13.5 years ago by ▴ 230
0
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10
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2.4k
views
How to convert from IRanges(List) to Rle(List)
convert IRanges convert IRanges
updated 13.5 years ago by 25k • written 13.5 years ago by ★ 1.2k
0
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0
replies
812
views
IRAnges compile error
IRanges IRanges
13.6 years ago Francoise.LECOMTE@biogemma.com ▴ 10
0
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0
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1.2k
views
Installing GenomicRanges require a version of IRanges unavailable
IRanges BiocInstaller IRanges BiocInstaller
13.7 years ago Duhaime Johanne ▴ 100
0
votes
0
replies
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
2
replies
1.1k
views
Integer overflow when summing an 'integer' Rle
Coverage IRanges Coverage IRanges
updated 13.7 years ago by 16k • written 13.7 years ago by ★ 1.2k
0
votes
1
reply
1.1k
views
htSeqTools - filtered reads > BED?
IRanges htSeqTools IRanges htSeqTools
updated 13.7 years ago by ★ 11k • written 13.7 years ago by ▴ 70
0
votes
0
replies
698
views
Bioconductor Digest, Vol 107, Issue 1
SNP Annotation probe affy biomaRt IRanges SNP Annotation probe affy biomaRt IRanges
13.8 years ago Peter Haverty ▴ 20
0
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4
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6.0k
views
GRanges - coercion from dataframe
convert IRanges convert IRanges
13.9 years ago Fahim Md ▴ 250
0
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1
reply
1.7k
views
RE : RE : rsamtools installation
Cancer Biostrings IRanges Rsamtools BiocInstaller Cancer Biostrings IRanges Rsamtools
updated 13.9 years ago by ▴ 140 • written 13.9 years ago by 25k
275 results • Page 4 of 6
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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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