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Showing :
bsgenome
•
reset
0
votes
0
replies
28
views
how to construct a SNPlocs-class by myself
BSgenome
SNPlocs
3 days ago
shangguandong1996
▴ 20
2
votes
4
replies
82
views
BSGenome Forge for non-model organism
BSGenomeForge
BSGenome
updated 6 days ago by
Hervé Pagès
14k • written 7 days ago by
sieminsk
• 0
0
votes
3
replies
236
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 3 months ago by
anamaria
▴ 10 • written 4 months ago by
sophie.harrington
• 0
2
votes
2
replies
178
views
Forging a BSGenome
BSgenome
microtus
forging
updated 4 months ago by
Hervé Pagès
14k • written 4 months ago by
A.J.
• 0
1
vote
4
replies
174
views
forging a BSgenome data package - Seed file issue
seedfiles
BSgenome
5 months ago
n.mary
• 0
2
votes
2
replies
177
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges
GenomeInfoDb
BSgenome
isCircular
updated 5 months ago by
Hervé Pagès
14k • written 6 months ago by
Chris Seidel
▴ 50
0
votes
3
replies
159
views
submitting a BSgenome package
BSgenome
updated 5 months ago by
Hervé Pagès
14k • written 5 months ago by
deisianyufg
• 0
0
votes
3
replies
285
views
Error in Forge the target package (BSgenome)
software error
BSgenome
7 months ago • updated 5 months ago
jiazhou0116
• 0
1
vote
1
reply
161
views
About generating a seed file (DCF format) for forging a BSgenome
software error
BSgenome
updated 6 months ago by
Hervé Pagès
14k • written 7 months ago by
jiazhou0116
• 0
0
votes
0
replies
79
views
Error in loading forged BSgenome
BSgenome
msgbsR
7 months ago
jiazhou0116
• 0
0
votes
1
reply
95
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements
IRanges
GenomicRanges
BSgenome
updated 7 months ago by
James W. MacDonald
56k • written 7 months ago by
vinod.acear
▴ 50
0
votes
1
reply
96
views
error when forging a BSgenome
BSgenome
updated 11 months ago by
shepherl
2.6k • written 11 months ago by
Didi
▴ 10
0
votes
4
replies
227
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome
MutationalPatterns
12 months ago • updated 11 months ago
sibyl.bertrand
• 0
0
votes
2
replies
121
views
vmatchPattern error using a DNA string and BSgenome
Biostrings
vmatchPattern
BSgenome
12 months ago
mb2subi
• 0
2
votes
6
replies
159
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation
mmul10
BSgenome
updated 16 months ago by
Hervé Pagès
14k • written 16 months ago by
P Darakjian
▴ 40
1
vote
0
replies
138
views
News:
New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome
News
16 months ago
Hervé Pagès
14k
2
votes
1
reply
103
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 17 months ago by
James W. MacDonald
56k • written 17 months ago by
Aditya
▴ 120
0
votes
6
replies
1.2k
views
Error while attempting to forge BSgenome data package
bsgenome
ggbio
updated 17 months ago by
serfraz.saad
• 0 • written 6.5 years ago by
pterry
• 0
3
votes
15
replies
388
views
Error in creating BSGenome package
BSGenome
updated 18 months ago by
James W. MacDonald
56k • written 18 months ago by
zen
• 0
0
votes
3
replies
295
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome
methods
GenomicRanges
19 months ago
Aditya
▴ 120
2
votes
3
replies
178
views
What is the use of a masked BSgenome?
BSgenome
BSgenome.Mmusculus.UCSC.mm10::Mmusculus
Biostrings
updated 19 months ago by
shepherl
2.6k • written 20 months ago by
Aditya
▴ 120
1
vote
2
replies
214
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome
GenomicRanges
updated 19 months ago by
Michael Lawrence
11k • written 19 months ago by
Aditya
▴ 120
0
votes
2
replies
231
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome
Bsgenome.Mmusculus.UCSC.mm10
20 months ago • updated 19 months ago
Aditya
▴ 120
1
vote
6
replies
638
views
How to subset a BSgenome
BSgenome
BSgenome.Mmusculus.UCSC.mm10
updated 20 months ago by
shepherl
2.6k • written 20 months ago by
Aditya
▴ 120
0
votes
6
replies
236
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair
BSgenome
Biostrings
BSgenome.Hsapiens.UCSC.hg19
updated 23 months ago by
James W. MacDonald
56k • written 23 months ago by
svetlana.gorokhova
• 0
0
votes
1
reply
216
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome
forgebsgenome
getSeqSrcpaths
2.1 years ago
tguerreroa90
• 0
2
votes
1
reply
257
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb
GRanges
BSGenome
variant annotation
updated 2.1 years ago by
James W. MacDonald
56k • written 2.1 years ago by
jacorvar
▴ 40
0
votes
9
replies
360
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq
BSgenome
BSgenomeForge
updated 2.1 years ago by
Julie Zhu
★ 4.3k • written 2.1 years ago by
danielle.bilodeau
• 0
2
votes
2
replies
502
views
BSgenome package building
bsgenome
updated 2.5 years ago by
James W. MacDonald
56k • written 2.5 years ago by
oussama.badad
• 0
3
votes
5
replies
645
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 2.6 years ago by
Hervé Pagès
14k • written 2.7 years ago by
svlachavas
▴ 780
0
votes
5
replies
459
views
Custom BSgenome with makeTxDbFromGFF
bsgenome
genomicfeatures
2.7 years ago
michael.weber.1
• 0
6
votes
3
replies
669
views
News:
New Bioconductor package for dbSNP151
SNPlocs.Hsapiens.dbSNP151.GRCh38
BSgenome
News
2.8 years ago
Hervé Pagès
14k
0
votes
1
reply
326
views
extract codon position via BSgenome
bsgenome
updated 2.8 years ago by
Hervé Pagès
14k • written 2.8 years ago by
k.rajain1212
• 0
1
vote
12
replies
1.4k
views
error in loadFun(x,seqname,ranges). BSgenome.Hsapiens.UCSC.hg19
bsgenome
updated 2.9 years ago by
James W. MacDonald
56k • written 2.9 years ago by
sophialovechan
▴ 10
1
vote
6
replies
661
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 3.1 years ago by
Lukas Chavez
▴ 550 • written 3.1 years ago by
vjain
• 0
2
votes
3
replies
541
views
What's the best way to retrieve the sizes (lengths) of chromosomes for a reference genome assembly?
bsgenome
chromosome
reference genome
updated 3.1 years ago by
Hervé Pagès
14k • written 3.1 years ago by
Nathan Sheffield
▴ 10
2
votes
1
reply
466
views
Using 'BSgenome::export' to write each chromosome of an organism into separate files
bsgenome
biocgenerics
bsapply
export
updated 3.1 years ago by
James W. MacDonald
56k • written 3.1 years ago by
ረ
• 0
0
votes
1
reply
910
views
How to name the custom genome in karyoploteR ?
software error
R
bsgenome
karyoploter
updated 3.4 years ago by
bernatgel
▴ 130 • written 3.4 years ago by
kirannbishwa01
• 0
0
votes
1
reply
767
views
add new genome as Bsgenome object
bsgenome
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
sneider.gutierrez01
• 0
0
votes
2
replies
607
views
BSgenome.Dmelanogaster.UCSC.dm6 annotation issue
bsgenome
BSgenome.Dmelanogaster.UCSC.dm6
3.6 years ago
jbeira
• 0
1
vote
3
replies
1.1k
views
BSgenome Sscrofa 11.1
sus scrofa
bsgenome
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
MartaG
• 0
4
votes
1
reply
1.0k
views
Getting "negative length vectors are not allowed" error in BSgenome::getSeq
BSgenome
getSeq
updated 3.7 years ago by
Martin Morgan
25k • written 3.7 years ago by
rubi
▴ 90
4
votes
3
replies
852
views
Extracting sequences from BSgenomeViews object
sequence
bsgenome
updated 3.7 years ago by
Martin Morgan
25k • written 3.7 years ago by
nicola.romano
▴ 10
0
votes
2
replies
1.0k
views
add annotation features to BSgenome or txdb package
bsgenome
txdb
annotation
orgdb
3.7 years ago
Didi
▴ 10
2
votes
5
replies
1.1k
views
Forge a BSgenome data package
bsgenome
bsgenome forge
4.2 years ago • updated 3.7 years ago
jodiera
• 0
1
vote
8
replies
800
views
CRISPRseek with genome not available in BSgenome
bsgenome
crisprseek
updated 3.8 years ago by
Julie Zhu
★ 4.3k • written 4.1 years ago by
millepattes.intersites
• 0
0
votes
2
replies
569
views
Human reference primary assembly and masking using BioStrings and BSgenome
biostrings
R
bsgenome
3.8 years ago
rockyb
• 0
5
votes
9
replies
1.8k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC
bsgenome
phastcons
rtracklayer
updated 3.9 years ago by
Ou, Jianhong
★ 1.2k • written 3.9 years ago by
crysis405
▴ 10
1
vote
7
replies
1.0k
views
Mapping Probes to a Genome
BSgenome
biostrings
probe mapping
updated 4.0 years ago by
holgerbrandl
▴ 10 • written 4.6 years ago by
Dario Strbenac
★ 1.5k
0
votes
4
replies
820
views
BS genome non-model organism
bsgenome
4.2 years ago • updated 4.1 years ago
minie
• 0
326 results • Page
1 of 7
Recent ...
Replies
Answer: DepMap copy number
by
Laurent Gatto
1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp
by
James W. MacDonald
56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq
by
Naomi Altman
★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile
by
Mike Smith
★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db
by
Xulei Huo
• 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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