Showing : BSGenome • reset
1
vote
6
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706
views
Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 7 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
4
replies
500
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
5 months ago • updated 10 weeks ago mat149 ▴ 70
1
vote
3
replies
563
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 6 months ago by • 0
0
votes
3
replies
668
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
0
votes
4
replies
898
views
BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
4
replies
724
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 10 months ago by 16k • written 11 months ago by • 0
1
vote
1
reply
517
views
add genome to BSgenome
bsgenome
updated 16 months ago by 3.8k • written 17 months ago by ▴ 10
2
votes
2
replies
1.7k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
18 months ago Mog • 0
9
votes
5
replies
1.4k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 18 months ago by 65k • written 18 months ago by • 0
0
votes
2
replies
5.0k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 19 months ago by ★ 1.6k • written 19 months ago by • 0
2
votes
3
replies
845
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 3 months ago by • 0 • written 23 months ago by ▴ 10
1
vote
1
reply
739
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 24 months ago by 16k • written 24 months ago by • 0
1
vote
0
replies
786
views
News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
2.0 years ago Hervé Pagès 16k
1
vote
1
reply
939
views
Fail to install BSgenome and library
BSgenome Celegans
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
1
vote
0
replies
766
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.0 years ago Charles Plessy ▴ 180
2
votes
4
replies
1.1k
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
2.1 years ago alain.corvisier • 0
2
votes
1
reply
813
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 2.2 years ago by 16k • written 2.2 years ago by ▴ 180
1
vote
5
replies
1.3k
views
submitting a BSgenome package
BSgenome
3.5 years ago • updated 2.2 years ago deisianyufg • 0
1
vote
2
replies
964
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
2.4 years ago geo.vogler ▴ 10
1
vote
2
replies
902
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 2.9 years ago by 16k • written 3.0 years ago by • 0
2
votes
7
replies
1.5k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
3
votes
5
replies
1.2k
views
unable to forge custom BSgenome after update
BSgenome
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 80
0
votes
0
replies
644
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.0 years ago Guandong Shang ▴ 40
2
votes
4
replies
1.7k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
0
votes
3
replies
1.7k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 3.3 years ago by ▴ 10 • written 3.4 years ago by • 0
3
votes
2
replies
2.1k
views
Forging a BSGenome
BSgenome microtus forging
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 20
1
vote
4
replies
1.5k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
3.4 years ago n.mary • 0
2
votes
2
replies
1.5k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 3.4 years ago by 16k • written 3.6 years ago by ▴ 80
0
votes
3
replies
1.4k
views
Error in Forge the target package (BSgenome)
software error BSgenome
3.6 years ago • updated 3.5 years ago jiazhou0116 • 0
1
vote
1
reply
955
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
0
votes
0
replies
601
views
Error in loading forged BSgenome
BSgenome msgbsR
3.6 years ago jiazhou0116 • 0
0
votes
1
reply
1.0k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 50
0
votes
1
reply
907
views
error when forging a BSgenome
BSgenome
updated 3.9 years ago by 3.8k • written 3.9 years ago by ▴ 10
0
votes
4
replies
1.8k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
4.1 years ago • updated 4.0 years ago sibyl.bertrand • 0
0
votes
2
replies
964
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.0 years ago mb2subi • 0
2
votes
6
replies
1.1k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 4.4 years ago by 16k • written 4.4 years ago by ▴ 40
1
vote
0
replies
734
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
4.4 years ago Hervé Pagès 16k
2
votes
1
reply
588
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 160
0
votes
6
replies
2.3k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 4.5 years ago by • 0 • written 9.5 years ago by • 0
3
votes
15
replies
2.1k
views
Error in creating BSGenome package
BSGenome
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
0
votes
3
replies
1.2k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
4.6 years ago Aditya ▴ 160
2
votes
3
replies
1.2k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 4.6 years ago by 3.8k • written 4.7 years ago by ▴ 160
1
vote
2
replies
937
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 4.6 years ago by ★ 11k • written 4.6 years ago by ▴ 160
0
votes
2
replies
992
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
4.7 years ago • updated 4.6 years ago Aditya ▴ 160
1
vote
6
replies
2.4k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 4.7 years ago by 3.8k • written 4.7 years ago by ▴ 160
0
votes
6
replies
1.1k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 4.9 years ago by 65k • written 4.9 years ago by • 0
0
votes
1
reply
879
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
5.1 years ago tguerreroa90 • 0
2
votes
1
reply
876
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 40
0
votes
9
replies
1.5k
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 5.1 years ago by ★ 4.3k • written 5.1 years ago by • 0
2
votes
2
replies
1.3k
views
BSgenome package building
bsgenome
updated 5.5 years ago by 65k • written 5.5 years ago by • 0
50 results • Page 1 of 1
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Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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