Showing : BSgenome • reset
4
votes
2
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2.0k
views
Ignoring N's on Ends of the Chromosome When Using matchPattern
bsgenome matchPattern
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 20
7
votes
6
replies
4.5k
views
How to find TF binding sites for particular TF's within +- 1000 bases of gene TSS for all genes in human genome?
bsgenome transcription factor binding site enrichment analysis matchpwm
10.3 years ago duncp92 ▴ 20
0
votes
1
reply
1.5k
views
Request: Add Macaca fascicularis genome to BSgenome
bsgenome genomes
updated 10.3 years ago by 16k • written 10.3 years ago by • 0
0
votes
5
replies
6.7k
views
Problem in BSgenome.Hsapiens.UCSC.hg19 Installation
bsgenome installation software error
updated 10.3 years ago by 25k • written 10.3 years ago by • 0
0
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1
reply
2.1k
views
Error of BSgenome.Hsapiens.UCSC.hg19 Installation
bsgenome software error
10.3 years ago ltian • 0
1
vote
11
replies
2.5k
views
Does BSgenome.Dmelanogaster.UCSC.dm2 maintain non-coding RNAs?
dm2 bsgenome noncoding RNA
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 20
0
votes
2
replies
1.8k
views
RCircos 2D track plot for a small region of genome
BSgenome BSgenome BSgenome BSgenome
updated 10.5 years ago by ▴ 50 • written 11.7 years ago by ★ 13k
1
vote
1
reply
1.7k
views
Conversion of BSgenome format to GRanges format?
bsgenome granges bam
updated 10.6 years ago by 68k • written 10.6 years ago by • 0
0
votes
6
replies
1.6k
views
Forging a BSgenome with lots of seqnames fails
bsgenome
10.7 years ago • updated 10.6 years ago Ryan C. Thompson ★ 7.9k
0
votes
2
replies
2.9k
views
BSgenome forging -- not valid BSgenomeDataPkgSeed slots
bsgenome
10.7 years ago qiwang1993 • 0
6
votes
2
replies
6.2k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome genomeinfodb transcriptdb
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 760
1
vote
2
replies
2.7k
views
Finding mismatches between reads and reference sequence
bsgenome cigar alignment
updated 10.8 years ago by 16k • written 10.8 years ago by ▴ 40
2
votes
2
replies
2.3k
views
Views on BSgenome object
BSgenome
10.8 years ago Kasper Daniel Hansen ★ 6.5k
2
votes
1
reply
2.6k
views
getSeq with GRanges object error: function not found
biostrings bsgenome granges
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 20
0
votes
5
replies
3.0k
views
Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome
BSgenome convert BSgenome PWMEnrich MotifDb
updated 11.0 years ago by ▴ 80 • written 11.0 years ago by ▴ 50
0
votes
0
replies
1.4k
views
subseq with iranges on reverse strand
Cancer BSgenome BSgenome IRanges Cancer BSgenome BSgenome IRanges
11.1 years ago Hervé Pagès 16k
0
votes
0
replies
1.3k
views
CRISPRseek: searchHits() optimization
Preprocessing BSgenome safe BSgenome CRISPRseek Preprocessing BSgenome safe BSgenome
11.1 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.3k
views
NuPoP cannot recognize my fasta file
BSgenome BSgenome NuPoP BSgenome BSgenome NuPoP
updated 11.1 years ago by ▴ 90 • written 11.1 years ago by ★ 13k
0
votes
1
reply
1.6k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ★ 13k
0
votes
3
replies
1.4k
views
SomaticSignatures: could not find function "motifMatrix"
BSgenome BSgenome BSgenome BSgenome
updated 11.2 years ago by ★ 1.3k • written 11.2 years ago by ★ 13k
0
votes
2
replies
2.1k
views
BSgenome
Homo sapiens BSgenome BSgenome Homo sapiens BSgenome BSgenome
updated 11.2 years ago by 68k • written 11.2 years ago by ▴ 290
0
votes
1
reply
1.6k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 11.2 years ago by 16k • written 11.2 years ago by ▴ 90
0
votes
1
reply
940
views
singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
11.2 years ago Hervé Pagès 16k
0
votes
1
reply
1.1k
views
Thread safety of BSgenome getSeq()
BSgenome BSgenome BSgenome BSgenome
updated 11.2 years ago by 16k • written 11.3 years ago by ▴ 90
0
votes
3
replies
2.2k
views
Creating a package
Saccharomyces cerevisiae BSgenome Biostrings BSgenome Saccharomyces cerevisiae BSgenome
updated 11.3 years ago by 68k • written 11.3 years ago by ★ 13k
0
votes
3
replies
2.9k
views
featureCounts segfault
Annotation BSgenome BSgenome Rsubread Annotation BSgenome BSgenome Rsubread
updated 11.3 years ago by ★ 3.6k • written 11.4 years ago by ★ 7.9k
0
votes
1
reply
1.5k
views
error when coercing GenomeData to RangedData: 'no method or default for coercing “XStringViews” to “RangedData”'
BSgenome BSgenome BSgenome BSgenome
updated 11.4 years ago by ★ 11k • written 11.4 years ago by ▴ 40
0
votes
0
replies
756
views
singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big
BSgenome BSgenome BSgenome BSgenome
11.4 years ago Guest User ★ 13k
0
votes
1
reply
2.4k
views
It works! RE: So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer
updated 11.4 years ago by ▴ 570 • written 11.4 years ago by ▴ 220
0
votes
0
replies
1.7k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
11.4 years ago Guest User ★ 13k
0
votes
0
replies
1.9k
views
Trying to use BSgenome.Hsapiens.NCBI.GRCh38
Cancer BSgenome BSgenome genomes Cancer BSgenome BSgenome genomes
11.4 years ago Hervé Pagès 16k
0
votes
1
reply
2.0k
views
So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer
updated 11.5 years ago by ▴ 570 • written 11.5 years ago by ▴ 220
0
votes
5
replies
2.4k
views
Rsamtools filtering bam file: RE: MEDIPS.createSet error
GO BSgenome BSgenome Rsamtools genomes MEDIPS GO BSgenome BSgenome Rsamtools genomes
updated 11.5 years ago by 25k • written 11.5 years ago by ▴ 220
0
votes
2
replies
1.5k
views
MEDIPS.createSet error
BSgenome BSgenome Rsamtools MEDIPS BSgenome BSgenome Rsamtools MEDIPS
updated 11.5 years ago by ▴ 570 • written 11.5 years ago by ▴ 220
0
votes
3
replies
1.3k
views
Cannot find the package created by pdInfoBuilder package
Annotation BSgenome probe BSgenome Annotation BSgenome probe BSgenome
updated 11.5 years ago by ★ 8.2k • written 11.5 years ago by ★ 13k
0
votes
5
replies
2.6k
views
MEDIPS.createSet error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 11.5 years ago by ▴ 570 • written 11.5 years ago by ▴ 220
0
votes
0
replies
1.2k
views
Repitools - featureScores - mappability Bsgenome object
BSgenome BSgenome Repitools BSgenome BSgenome Repitools
11.5 years ago Dario Strbenac ★ 1.6k
0
votes
7
replies
2.5k
views
QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
Alignment Rattus norvegicus BSgenome BSgenome QuasR Alignment Rattus norvegicus BSgenome
updated 11.5 years ago by 16k • written 11.5 years ago by ★ 4.1k
0
votes
2
replies
1.1k
views
pileupAsGranges invalid times error
BSgenome BSgenome BSgenome BSgenome
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Repitools - featureScores - mappability Bsgenome object
BSgenome BSgenome Repitools BSgenome BSgenome Repitools
11.5 years ago Jaritz,Markus ▴ 20
0
votes
1
reply
1.6k
views
I need help making a dcf seed file to encapsulate a genome assembly im using.
Cancer Yeast BSgenome BSgenome Cancer Yeast BSgenome BSgenome
updated 11.7 years ago by ▴ 10 • written 11.7 years ago by 16k
0
votes
2
replies
1.5k
views
Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?
Annotation GO BSgenome TranscriptDb BSgenome GenomicFeatures Annotation GO BSgenome
updated 11.7 years ago by 16k • written 11.7 years ago by ▴ 60
0
votes
1
reply
1.1k
views
forgeSeqFiles
Organism BSgenome BSgenome Organism BSgenome BSgenome
updated 11.7 years ago by 16k • written 11.7 years ago by ★ 13k
0
votes
2
replies
1.8k
views
Aha: different error may be a clue: RE: separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
votes
6
replies
2.2k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
votes
3
replies
1.6k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
votes
0
replies
1.2k
views
It works: RE: using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
11.7 years ago Vining, Kelly ▴ 220
0
votes
1
reply
1.5k
views
using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
votes
1
reply
5.6k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 11.7 years ago by ▴ 280 • written 11.7 years ago by 16k
0
votes
5
replies
2.0k
views
matchPattern vmatchPattern vectorised
BSgenome BSgenome BSgenome BSgenome
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ★ 13k
348 results • Page 3 of 7
Recent ...
Replies
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0
Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…
Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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