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Showing :
bsgenome
•
reset
1
vote
1
reply
115
views
add genome to BSgenome
bsgenome
updated 8 weeks ago by
shepherl
3.4k • written 9 weeks ago by
Luigi
▴ 10
2
votes
2
replies
315
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
3 months ago
Mog
• 0
9
votes
5
replies
363
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10.
karyoploteR
BSgenome
updated 4 months ago by
James W. MacDonald
62k • written 4 months ago by
rtt100
• 0
0
votes
2
replies
1.1k
views
Any tools to convert .gff to .gtf format
AnnotationData
CrispRdesignR
BSgenome
updated 4 months ago by
Malcolm Cook
★ 1.6k • written 4 months ago by
Manoj Kumar R
• 0
2
votes
2
replies
310
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 7 days ago by
Thomas
• 0 • written 8 months ago by
remerandmaxence
▴ 10
1
vote
1
reply
282
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 9 months ago by
Hervé Pagès
16k • written 9 months ago by
liangdan312
• 0
1
vote
0
replies
316
views
News:
BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome
dbSNP
T2T-CHM13v2.0
SNPlocs
9 months ago
Hervé Pagès
16k
1
vote
1
reply
406
views
Fail to install BSgenome and library
BSgenome
Celegans
updated 9 months ago by
Hervé Pagès
16k • written 9 months ago by
Tsung-Han
• 0
1
vote
0
replies
286
views
How about a getSeq() method for GRanges ?
GenomicRanges
BSGenome
9 months ago
Charles Plessy
▴ 170
2
votes
4
replies
416
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome
seqinfo
10 months ago
alain.corvisier
• 0
2
votes
1
reply
359
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 12 months ago by
Hervé Pagès
16k • written 12 months ago by
Charles Plessy
▴ 170
1
vote
5
replies
786
views
submitting a BSgenome package
BSgenome
2.2 years ago • updated 12 months ago
deisianyufg
• 0
1
vote
2
replies
490
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome
Forge
14 months ago
geo.vogler
▴ 10
1
vote
2
replies
511
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 20 months ago by
Hervé Pagès
16k • written 21 months ago by
Imad
• 0
2
votes
7
replies
871
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 21 months ago by
Hervé Pagès
16k • written 21 months ago by
aybuge.altay
• 0
3
votes
5
replies
650
views
unable to forge custom BSgenome after update
BSgenome
updated 21 months ago by
Hervé Pagès
16k • written 21 months ago by
Chris Seidel
▴ 80
0
votes
0
replies
333
views
how to construct a SNPlocs-class by myself
BSgenome
SNPlocs
21 months ago
Guandong Shang
▴ 40
2
votes
4
replies
863
views
BSGenome Forge for non-model organism
BSGenomeForge
BSGenome
updated 21 months ago by
Hervé Pagès
16k • written 21 months ago by
sieminsk
• 0
0
votes
3
replies
980
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 2.1 years ago by
anamaria
▴ 10 • written 2.2 years ago by
sophie.harrington
• 0
2
votes
2
replies
1.1k
views
Forging a BSGenome
BSgenome
microtus
forging
updated 2.1 years ago by
Hervé Pagès
16k • written 2.1 years ago by
A.J.
▴ 20
1
vote
4
replies
793
views
forging a BSgenome data package - Seed file issue
seedfiles
BSgenome
2.2 years ago
n.mary
• 0
2
votes
2
replies
792
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges
GenomeInfoDb
BSgenome
isCircular
updated 2.2 years ago by
Hervé Pagès
16k • written 2.3 years ago by
Chris Seidel
▴ 80
0
votes
3
replies
917
views
Error in Forge the target package (BSgenome)
software error
BSgenome
2.4 years ago • updated 2.2 years ago
jiazhou0116
• 0
1
vote
1
reply
536
views
About generating a seed file (DCF format) for forging a BSgenome
software error
BSgenome
updated 2.4 years ago by
Hervé Pagès
16k • written 2.4 years ago by
jiazhou0116
• 0
0
votes
0
replies
328
views
Error in loading forged BSgenome
BSgenome
msgbsR
2.4 years ago
jiazhou0116
• 0
0
votes
1
reply
500
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements
IRanges
GenomicRanges
BSgenome
updated 2.4 years ago by
James W. MacDonald
62k • written 2.4 years ago by
vinod.acear
▴ 50
0
votes
1
reply
444
views
error when forging a BSgenome
BSgenome
updated 2.7 years ago by
shepherl
3.4k • written 2.7 years ago by
Didi
▴ 10
0
votes
4
replies
969
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome
MutationalPatterns
2.8 years ago
sibyl.bertrand
• 0
0
votes
2
replies
484
views
vmatchPattern error using a DNA string and BSgenome
Biostrings
vmatchPattern
BSgenome
2.8 years ago
mb2subi
• 0
2
votes
6
replies
601
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation
mmul10
BSgenome
updated 3.1 years ago by
Hervé Pagès
16k • written 3.1 years ago by
P Darakjian
▴ 40
1
vote
0
replies
414
views
News:
New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome
News
3.1 years ago
Hervé Pagès
16k
2
votes
1
reply
301
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 3.2 years ago by
James W. MacDonald
62k • written 3.2 years ago by
Aditya
▴ 140
0
votes
6
replies
1.9k
views
Error while attempting to forge BSgenome data package
bsgenome
ggbio
updated 3.2 years ago by
serfraz.saad
• 0 • written 8.3 years ago by
pterry
• 0
3
votes
15
replies
1.1k
views
Error in creating BSGenome package
BSGenome
updated 3.3 years ago by
James W. MacDonald
62k • written 3.3 years ago by
zen
• 0
0
votes
3
replies
725
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome
methods
GenomicRanges
3.4 years ago
Aditya
▴ 140
2
votes
3
replies
546
views
What is the use of a masked BSgenome?
BSgenome
BSgenome.Mmusculus.UCSC.mm10::Mmusculus
Biostrings
updated 3.4 years ago by
shepherl
3.4k • written 3.4 years ago by
Aditya
▴ 140
1
vote
2
replies
538
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome
GenomicRanges
updated 3.4 years ago by
Michael Lawrence
11k • written 3.4 years ago by
Aditya
▴ 140
0
votes
2
replies
572
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome
Bsgenome.Mmusculus.UCSC.mm10
3.5 years ago • updated 3.4 years ago
Aditya
▴ 140
1
vote
6
replies
1.4k
views
How to subset a BSgenome
BSgenome
BSgenome.Mmusculus.UCSC.mm10
updated 3.5 years ago by
shepherl
3.4k • written 3.5 years ago by
Aditya
▴ 140
0
votes
6
replies
639
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair
BSgenome
Biostrings
BSgenome.Hsapiens.UCSC.hg19
updated 3.7 years ago by
James W. MacDonald
62k • written 3.7 years ago by
svetlana.gorokhova
• 0
0
votes
1
reply
498
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome
forgebsgenome
getSeqSrcpaths
3.8 years ago
tguerreroa90
• 0
2
votes
1
reply
534
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb
GRanges
BSGenome
variant annotation
updated 3.9 years ago by
James W. MacDonald
62k • written 3.9 years ago by
jacorvar
▴ 40
0
votes
9
replies
855
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq
BSgenome
BSgenomeForge
updated 3.9 years ago by
Julie Zhu
★ 4.3k • written 3.9 years ago by
danielle.bilodeau
• 0
2
votes
2
replies
947
views
BSgenome package building
bsgenome
updated 4.3 years ago by
James W. MacDonald
62k • written 4.3 years ago by
oussama.badad
• 0
3
votes
5
replies
1.1k
views
Include and implement a new reference genome option in the R package BSgenome for downstream variant calling analysis
bsgenome
variant calling
whole exome sequence
gencode
reference genome
updated 4.4 years ago by
Hervé Pagès
16k • written 4.4 years ago by
svlachavas
▴ 800
0
votes
5
replies
821
views
Custom BSgenome with makeTxDbFromGFF
bsgenome
genomicfeatures
4.5 years ago
michael.weber.1
• 0
6
votes
3
replies
1.3k
views
News:
New Bioconductor package for dbSNP151
SNPlocs.Hsapiens.dbSNP151.GRCh38
BSgenome
News
4.6 years ago
Hervé Pagès
16k
0
votes
1
reply
599
views
extract codon position via BSgenome
bsgenome
updated 4.6 years ago by
Hervé Pagès
16k • written 4.6 years ago by
k.rajain1212
• 0
1
vote
12
replies
2.8k
views
error in loadFun(x,seqname,ranges). BSgenome.Hsapiens.UCSC.hg19
bsgenome
updated 4.7 years ago by
James W. MacDonald
62k • written 4.7 years ago by
sophialovechan
▴ 10
1
vote
6
replies
1.1k
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 4.9 years ago by
Lukas Chavez
▴ 570 • written 4.9 years ago by
vjain
• 0
50 results • Page
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Comment: transcript name mapping between human and mouse
by
Eric
• 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Bernardo
• 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report
by
Okan
• 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
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Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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