Showing : genomes • reset
0
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1
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404
views
I am having issues with bowtie2_build
genomes bowtiew Index
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
451
views
affymetrix
genomes Annotation
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
458
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Correlation between gene clusters
genomes RNASeqData
written 11 months ago by • 0
0
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0
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5
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Spam: <img/src/onerror=alert&#xFEFF;(1337)>
genomes rgu34cprobe
12 months ago <img/src/onerror=alert&#xFEFF;(1337)> 0
2
votes
5
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1.9k
views
Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ("trying to load regions beyond the boundaries of non-circular sequenc…
genomes BSgenome.Mmusculus.UCSC.mm39
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
3
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913
views
ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 14 months ago by • 0
0
votes
0
replies
333
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
13 months ago user_bioinfo • 0
0
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0
replies
395
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
13 months ago brayas13 • 0
0
votes
1
reply
666
views
probe ID search for SNP (plink)
genomes
updated 13 months ago by 68k • written 13 months ago by • 0
1
vote
6
replies
1.8k
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 13 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
0
replies
601
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
14 months ago Fernanda • 0
0
votes
1
reply
495
views
For feline genome
genomes Analysisoffelinegenome
updated 14 months ago by 68k • written 14 months ago by • 0
2
votes
5
replies
1.2k
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
14 months ago ronin • 0
0
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0
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635
views
Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
14 months ago Ragnhild • 0
0
votes
0
replies
660
views
Job: Ensembl Job Vacancies
genomes Annotation GenomicVariation ensembldb
15 months ago Aleena_Ensembl ▴ 30
0
votes
0
replies
933
views
Job: Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics
genomes
2.1 years ago JP Cartailler ▴ 40
0
votes
0
replies
1.3k
views
Job: Bioinformatics Research Associate, Genomics and Genetics
genomes Genetics
2.1 years ago JP Cartailler ▴ 40
1
vote
1
reply
766
views
MSc student
genomes
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
0
votes
2
replies
4.2k
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
written 3.8 years ago by • 0
0
votes
0
replies
1.3k
views
How to assign custom colour codes for Multiple sequence alignment (MSA)?
Phylogenetics genomes R MultipleSequenceAlignment Bioconductor
4.3 years ago K. • 0
1
vote
0
replies
2.0k
views
Job: Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job computational biology genomes pathways machine learning Job
8.1 years ago bulfin.triona ▴ 10
0
votes
0
replies
1.5k
views
How to generate CpG island Unmasked.bed file format for finding CpG island shores and shelves?
bioconductor annotation rtracklayer genomes homo.sapiens
8.4 years ago sivabala76 • 0
0
votes
5
replies
2.2k
views
Extracting all possible annotations between two genomic coordinates
genomes
8.8 years ago KB ▴ 50
0
votes
0
replies
1.4k
views
vizualization of mutations
genomes SNP
9.2 years ago Bogdan ▴ 670
0
votes
0
replies
2.1k
views
Job: Postdoc / Computational Biologist for circulating tumor DNA/RNA profiling at Memorial Sloan Kettering Cancer Center MSKCC, New York
cancer sequencing genetics genomes diagnostic Job
9.3 years ago dtlabmskcc • 0
1
vote
1
reply
2.0k
views
GenomeViz
Proteomics genomes Proteomics genomes
updated 9.8 years ago by • 0 • written 20.9 years ago by ▴ 80
0
votes
1
reply
1.6k
views
Request: Add Macaca fascicularis genome to BSgenome
bsgenome genomes
updated 10.5 years ago by 16k • written 10.5 years ago by • 0
0
votes
0
replies
1.9k
views
Job: Harvard Medical School: Postdoctoral Opportunity
genomes Job
11.2 years ago Doe, Aimee ▴ 40
0
votes
8
replies
3.6k
views
Best practices to find intersection among variants
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 11.3 years ago by ★ 1.3k • written 11.3 years ago by ▴ 220
2
votes
3
replies
6.0k
views
Linkage disequilibrium with 1000 Genomes/HapMap
HapMap genomes HapMap genomes
11.4 years ago enricoferrero ▴ 680
0
votes
3
replies
2.0k
views
Elephant shark genome
Biostrings genomes Biostrings genomes
updated 11.6 years ago by 25k • written 11.6 years ago by ★ 13k
0
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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 11.6 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
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1
reply
2.0k
views
GOseq with ce6
GO Yeast Organism goseq genomes GO Yeast Organism goseq genomes
updated 11.7 years ago by ▴ 320 • written 11.7 years ago by ▴ 50
0
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0
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2.0k
views
Trying to use BSgenome.Hsapiens.NCBI.GRCh38
Cancer BSgenome BSgenome genomes Cancer BSgenome BSgenome genomes
11.7 years ago Hervé Pagès 16k
0
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1
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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 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
votes
5
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2.5k
views
Rsamtools filtering bam file: RE: MEDIPS.createSet error
GO BSgenome BSgenome Rsamtools genomes MEDIPS GO BSgenome BSgenome Rsamtools genomes
updated 11.7 years ago by 25k • written 11.7 years ago by ▴ 220
0
votes
3
replies
2.7k
views
Find enriched GO terms, given a list of GO terms of interest and background GO terms
Annotation GO topGO genomes Annotation GO topGO genomes
11.9 years ago Guest User ★ 13k
0
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1
reply
2.0k
views
makeTranscriptDbFromUCSC() error
genomes genomes
11.9 years ago Chris Cabanski ▴ 30
0
votes
2
replies
2.7k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription HapMap PolyPhen SIFT convert genomes ensemblVEP Transcription HapMap SIFT
updated 11.9 years ago by ★ 6.8k • written 11.9 years ago by ▴ 30
0
votes
1
reply
2.6k
views
Pairwise Alignment on Large Protein Sequence Data Set
Alignment genomes Alignment genomes
updated 12.0 years ago by 16k • written 12.0 years ago by ★ 13k
0
votes
0
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1.8k
views
Gviz and Leishmania genomes
rtracklayer genomes Gviz rtracklayer genomes Gviz
12.1 years ago florian.hahne@novartis.com ★ 1.6k
0
votes
0
replies
2.2k
views
Create a sample file /tab delimited file in QuasR
BSgenome convert BSgenome genomes QuasR BSgenome convert BSgenome genomes QuasR
12.1 years ago Michael Stadler ▴ 350
0
votes
1
reply
2.0k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
GO TranscriptDb goseq genomes GO TranscriptDb goseq genomes
updated 12.1 years ago by ★ 7.2k • written 12.1 years ago by ▴ 80
0
votes
1
reply
1.9k
views
Lifting over a bam file with Rsamtools and GenomicRanges
GenomicRanges genomes GenomicRanges genomes
updated 12.2 years ago by ★ 11k • written 12.2 years ago by ★ 13k
0
votes
0
replies
1.4k
views
SnpStats - STRING_ELT() error and Fst
genomes genomes
12.2 years ago Voke AO ▴ 760
0
votes
1
reply
1.6k
views
Working with non-type strain annotation
Proteomics GO genomes Proteomics GO genomes
updated 12.5 years ago by ★ 7.2k • written 12.6 years ago by ▴ 70
0
votes
8
replies
4.1k
views
QuasR: how to use an indexed reference genome?
BSgenome BSgenome genomes QuasR BSgenome BSgenome genomes QuasR
updated 12.6 years ago by ▴ 350 • written 12.6 years ago by ▴ 750
0
votes
2
replies
2.1k
views
QuasR special case alignment
Alignment genomes QuasR Alignment genomes QuasR
updated 12.6 years ago by ▴ 340 • written 12.6 years ago by ▴ 350
0
votes
6
replies
2.1k
views
coverage on very large ReadGappedAlignmentsObject
Coverage genomes Coverage genomes
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 360
0
votes
1
reply
2.3k
views
Help needed! What wrong with VariantAnnotation and TCGA vcfs
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 12.7 years ago by 25k • written 12.7 years ago by ▴ 340
115 results • Page 1 of 3
Recent ...
Replies
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
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Popular Question to James W. MacDonald 68k
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