Showing : bsgenome • reset
2
votes
2
replies
1.9k
views
"Wobble" patterns for genome searching using Biostrings
biostrings bsgenome motif RGYW
10.3 years ago fongchunchan ▴ 30
4
votes
2
replies
2.0k
views
Ignoring N's on Ends of the Chromosome When Using matchPattern
bsgenome matchPattern
updated 10.3 years ago by 16k • written 10.3 years ago by ▴ 20
7
votes
6
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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
10.4 years ago duncp92 ▴ 20
0
votes
1
reply
1.5k
views
Request: Add Macaca fascicularis genome to BSgenome
bsgenome genomes
updated 10.4 years ago by 16k • written 10.4 years ago by • 0
0
votes
5
replies
6.7k
views
Problem in BSgenome.Hsapiens.UCSC.hg19 Installation
bsgenome installation software error
updated 10.4 years ago by 25k • written 10.4 years ago by • 0
0
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1
reply
2.1k
views
Error of BSgenome.Hsapiens.UCSC.hg19 Installation
bsgenome software error
10.4 years ago ltian • 0
1
vote
11
replies
2.6k
views
Does BSgenome.Dmelanogaster.UCSC.dm2 maintain non-coding RNAs?
dm2 bsgenome noncoding RNA
updated 10.5 years ago by 16k • written 10.5 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 10.6 years ago by ▴ 50 • written 11.8 years ago by ★ 13k
1
vote
1
reply
1.7k
views
Conversion of BSgenome format to GRanges format?
bsgenome granges bam
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
0
votes
6
replies
1.7k
views
Forging a BSgenome with lots of seqnames fails
bsgenome
10.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
2
replies
2.9k
views
BSgenome forging -- not valid BSgenomeDataPkgSeed slots
bsgenome
10.8 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 10.8 years ago by 16k • written 10.8 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 10.9 years ago by ▴ 40
2
votes
2
replies
2.3k
views
Views on BSgenome object
BSgenome
10.9 years ago Kasper Daniel Hansen ★ 6.5k
2
votes
1
reply
2.7k
views
getSeq with GRanges object error: function not found
biostrings bsgenome granges
updated 11.1 years ago by 25k • written 11.1 years ago by ▴ 20
0
votes
5
replies
3.1k
views
Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome
BSgenome convert BSgenome PWMEnrich MotifDb
updated 11.1 years ago by ▴ 80 • written 11.1 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
11.2 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 11.2 years ago by ▴ 90 • written 11.2 years ago by ★ 13k
0
votes
1
reply
1.7k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 11.2 years ago by ▴ 570 • written 11.2 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 11.3 years ago by 68k • written 11.3 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 11.3 years ago by 16k • written 11.3 years ago by ▴ 90
0
votes
1
reply
955
views
singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
11.3 years ago Hervé Pagès 16k
0
votes
1
reply
1.1k
views
Thread safety of BSgenome getSeq()
BSgenome BSgenome BSgenome BSgenome
updated 11.3 years ago by 16k • written 11.4 years ago by ▴ 90
0
votes
3
replies
2.2k
views
Creating a package
Saccharomyces cerevisiae BSgenome Biostrings BSgenome Saccharomyces cerevisiae BSgenome
updated 11.4 years ago by 68k • written 11.4 years ago by ★ 13k
0
votes
3
replies
2.9k
views
featureCounts segfault
Annotation BSgenome BSgenome Rsubread Annotation BSgenome BSgenome Rsubread
updated 11.4 years ago by ★ 3.6k • written 11.4 years ago by ★ 7.9k
0
votes
1
reply
1.6k
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
765
views
singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big
BSgenome BSgenome BSgenome BSgenome
11.5 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 11.5 years ago by ▴ 570 • written 11.5 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
11.5 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
11.5 years ago Hervé Pagès 16k
0
votes
1
reply
2.1k
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 11.6 years ago by ★ 8.2k • written 11.6 years ago by ★ 13k
0
votes
5
replies
2.6k
views
MEDIPS.createSet error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 11.6 years ago by ▴ 570 • written 11.6 years ago by ▴ 220
0
votes
0
replies
1.2k
views
Repitools - featureScores - mappability Bsgenome object
BSgenome BSgenome Repitools BSgenome BSgenome Repitools
11.6 years ago Dario Strbenac ★ 1.6k
0
votes
7
replies
2.6k
views
QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
Alignment Rattus norvegicus BSgenome BSgenome QuasR Alignment Rattus norvegicus BSgenome
updated 11.6 years ago by 16k • written 11.6 years ago by ★ 4.1k
0
votes
2
replies
1.1k
views
pileupAsGranges invalid times error
BSgenome BSgenome BSgenome BSgenome
updated 11.6 years ago by ★ 11k • written 11.6 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Repitools - featureScores - mappability Bsgenome object
BSgenome BSgenome Repitools BSgenome BSgenome Repitools
11.6 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 11.8 years ago by ▴ 10 • written 11.8 years ago by 16k
0
votes
2
replies
1.6k
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 11.8 years ago by 16k • written 11.8 years ago by ▴ 60
0
votes
1
reply
1.2k
views
forgeSeqFiles
Organism BSgenome BSgenome Organism BSgenome BSgenome
updated 11.8 years ago by 16k • written 11.8 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 11.8 years ago by ▴ 570 • written 11.8 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 11.8 years ago by ▴ 570 • written 11.8 years ago by ▴ 220
0
votes
3
replies
1.7k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 11.8 years ago by ▴ 570 • written 11.8 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
11.8 years ago Vining, Kelly ▴ 220
0
votes
1
reply
1.5k
views
using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 11.8 years ago by ▴ 570 • written 11.8 years ago by ▴ 220
0
votes
1
reply
5.7k
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 11.8 years ago by ▴ 280 • written 11.8 years ago by 16k
349 results • Page 3 of 7
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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