Showing : Iranges • reset
0
votes
6
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1.1k
views
Merging RandData object with names on the IRanges part
IRanges IRanges
13.0 years ago Ulrike Goebel ▴ 110
5
votes
8
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6.5k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 6 months ago by • 0 • written 6.9 years ago by ▴ 50
3
votes
5
replies
875
views
Problem with svn_time() function on IRanges package - trying to run "exomePeak" package
iranges
6.9 years ago m.ghanatbari • 0
0
votes
8
replies
838
views
stranded findOverlaps
IRanges IRanges
updated 12.6 years ago by ▴ 50 • written 12.6 years ago by ★ 2.9k
4
votes
8
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1.5k
views
closest-features equivalent in Bioconductor for finding closest gene(s)
genomicranges granges iranges annotatepeak
updated 6.3 years ago by 11k • written 6.3 years ago by ▴ 70
0
votes
6
replies
4.9k
views
GRanges: problem with multiple seqnames and seqlengths
GRanges seqnames seqlengths IRanges
7.9 years ago topher.hamm • 0
0
votes
16
replies
3.2k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 8.7 years ago by 15k • written 8.7 years ago by ▴ 740
2
votes
10
replies
2.6k
views
Extract three types of intergenic regions
granges views annotation iranges
updated 6.8 years ago by ★ 1.7k • written 6.8 years ago by ▴ 50
0
votes
4
replies
1.2k
views
Getting first or last hit from a Hits object
IRanges GenomicRanges IRanges GenomicRanges
updated 8.8 years ago by 11k • written 8.8 years ago by ▴ 560
0
votes
11
replies
1.5k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
10.8 years ago Stefanie Ververs ▴ 70
0
votes
5
replies
880
views
HiTC importC not working
HiTC IRanges windows debian
updated 4.4 years ago by ▴ 260 • written 4.4 years ago by • 0
0
votes
8
replies
1.1k
views
IRanges problem: findOverlaps
IRanges IRanges
updated 10.1 years ago by ▴ 50 • written 10.1 years ago by ▴ 20
0
votes
3
replies
761
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 6.8 years ago by 15k • written 6.8 years ago by ▴ 50
0
votes
15
replies
1.1k
views
Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
bioconductor iranges s4vectors xvector r 3.3.2
updated 4.1 years ago by ▴ 10 • written 4.1 years ago by • 0
2
votes
4
replies
3.6k
views
Help with sliding window analysis on GRanges object
IRanges IRanges
8.4 years ago Stefano Iantorno ▴ 30
0
votes
4
replies
850
views
error in function reduce from girafe
Annotation annotate biomaRt IRanges girafe Annotation annotate biomaRt IRanges girafe
updated 12.1 years ago by ▴ 450 • written 12.2 years ago by ▴ 810
2
votes
5
replies
3.3k
views
unlist doesn't work for IRanges
iranges
updated 4.2 years ago by 60k • written 4.2 years ago by ▴ 450
1
vote
4
replies
1.9k
views
biocLite updating problem with Ubuntu 17.10
ubuntu biocgenerics s4vectors IRanges annotationdbi
updated 4.7 years ago by 25k • written 4.7 years ago by • 0
4
votes
2
replies
583
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
3.7 years ago foehn ▴ 80
6
votes
6
replies
997
views
Implementing fast mathematical and statistical operations on genomic variables in bioconductor
genomicranges biocgenerics rlelist genomicvars iranges
updated 4.9 years ago by 15k • written 4.9 years ago by ▴ 20
6
votes
3
replies
1.3k
views
how does coverage() works
biostrings coverage rle iranges
6.2 years ago likeeatingpizza ▴ 10
0
votes
3
replies
1.1k
views
Using IRanges to find gene TSS that overlap a window
iranges R granges
updated 5.0 years ago by • 0 • written 5.0 years ago by ▴ 20
7
votes
4
replies
1.4k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 4.9 years ago by 15k • written 4.9 years ago by ▴ 40
3
votes
2
replies
845
views
Using GRanges and IRanges to simply get all chromosome data
GRanges IRanges
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 20
0
votes
2
replies
687
views
Adding names to a IRanges object
Cancer IRanges Cancer IRanges
updated 13.6 years ago by ▴ 620 • written 13.6 years ago by ★ 1.9k
4
votes
17
replies
2.3k
views
How to construct a valid GRanges object from RCPP and pass back to R
GRanges IRanges RCPP Constructor
updated 4.8 years ago by ▴ 10 • written 4.9 years ago by ▴ 80
0
votes
8
replies
1.4k
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 9.7 years ago by 11k • written 9.7 years ago by 15k
0
votes
5
replies
854
views
IRanges causes bug in complete.cases
Regression IRanges Regression IRanges
updated 12.7 years ago by 11k • written 12.7 years ago by 6.5k
1
vote
3
replies
817
views
Error trying to run "seqlm" example
seqlm IRanges R namespace dmr analysis
6.1 years ago calen.p.ryan • 0
8
votes
12
replies
3.6k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 29 days ago by • 0 • written 7.4 years ago by ▴ 20
0
votes
3
replies
901
views
seqselect function in IRanges not working
IRanges IRanges
updated 12.3 years ago by 60k • written 12.3 years ago by ▴ 250
3
votes
4
replies
1.3k
views
Introns at transcript expression level
genomicfeatures iranges
updated 7.4 years ago by 15k • written 7.4 years ago by ▴ 20
2
votes
5
replies
1.0k
views
making a RleViewsList object gets slow with many chromosomes
views iranges rle
7.5 years ago Janet Young ▴ 740
0
votes
2
replies
1.9k
views
Coverage vs GC bias - how to?
Coverage BSgenome BSgenome IRanges Coverage BSgenome BSgenome IRanges
updated 11.9 years ago by ▴ 590 • written 11.9 years ago by ▴ 100
0
votes
6
replies
1.1k
views
iranges
IRanges IRanges
updated 8.0 years ago by ★ 6.7k • written 8.0 years ago by ▴ 680
1
vote
2
replies
695
views
IRanges vignette code comment
iranges
updated 8 weeks ago by • 0 • written 7.5 years ago by 37k
0
votes
2
replies
5.1k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 8.8 years ago by 11k • written 8.8 years ago by 15k
1
vote
5
replies
1.3k
views
'version' is missing error when running makeTxDbPackageFromUCSC
Cancer TranscriptDb IRanges GenomicFeatures Cancer TranscriptDb IRanges GenomicFeatures
updated 6.8 years ago by ▴ 10 • written 9.0 years ago by 15k
0
votes
4
replies
1.1k
views
help with flank()
IRanges IRanges
updated 11.8 years ago by 6.6k • written 11.8 years ago by ▴ 330
0
votes
3
replies
1.5k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 8.4 years ago by 15k • written 8.4 years ago by 11k
4
votes
3
replies
1.5k
views
Overlap the snps
overlap snps granges iranges
updated 7.9 years ago by 11k • written 7.9 years ago by ▴ 10
0
votes
2
replies
864
views
Fwd: BioStrings PairwiseAlignment deletion() insertion() function
Alignment Cancer Biostrings IRanges Alignment Cancer Biostrings IRanges
updated 8.9 years ago by ▴ 30 • written 8.9 years ago by 15k
0
votes
8
replies
1.3k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 8.5 years ago by 11k • written 8.5 years ago by ▴ 30
0
votes
8
replies
1.3k
views
good news and bad news
Infrastructure Cancer IRanges GenomicRanges Infrastructure Cancer IRanges GenomicRanges
updated 10.0 years ago by 13k • written 10.0 years ago by 15k
0
votes
16
replies
1.0k
views
IRanges is broken in Cygwin (mingw/math.h)
IRanges IRanges
updated 9.1 years ago by 11k • written 9.1 years ago by ▴ 620
0
votes
2
replies
1.1k
views
one problem about IRanges Package
simpleaffy IRanges simpleaffy IRanges
updated 11.8 years ago by 6.6k • written 11.8 years ago by ▴ 50
0
votes
2
replies
710
views
*Ranges paper published
Infrastructure IRanges GenomicFeatures GenomicRanges Infrastructure IRanges GenomicFeatures
updated 9.0 years ago by ★ 4.2k • written 9.0 years ago by 11k
0
votes
2
replies
626
views
annotating reads acording with position on mapping
Annotation annotate biomaRt IRanges Annotation annotate biomaRt IRanges
updated 12.3 years ago by ▴ 450 • written 12.3 years ago by ▴ 810
0
votes
4
replies
709
views
findOveraps suggestions
Cancer IRanges Cancer IRanges
updated 12.6 years ago by 11k • written 12.6 years ago by ▴ 740
0
votes
3
replies
733
views
IRanges: find containment and not just overlap
IRanges IRanges
updated 13.5 years ago by ▴ 620 • written 13.5 years ago by ▴ 210
50 results • Page 1 of 1
Recent ...
Replies
Comment: Error in Create switchAnalyzeRlist by bpshtiwan ▴ 10
Definitely, you are right. I Checked the ref file (cDNA fasta and gtf file ) gene Id is different. I downloaded both gtf and cDNA fasts fi…
Comment: errors in annotation by Josie • 0
OK thanks James. I'll send off an email to GenBank, see if they feel inclined to correct some errors.
Answer: Conversion of UniProt to Ensembl by James W. MacDonald 60k
I will provide an example below. But first, there is a vignette for biomaRt (actually two), and it has extensive examples of how to use the…
Comment: the difference between getGEO and getGEOSuppFiles by Fatemeh • 0
thank you!
Answer: the difference between getGEO and getGEOSuppFiles by James W. MacDonald 60k
When submitting data to GEO, you are supposed to provide both the raw data and a matrix of processed data. When you use `getGEO` you get th…
Votes
Answer: Error in Create switchAnalyzeRlist
Answer: Error in Create switchAnalyzeRlist
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
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