Showing : genomes • reset
0
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1
reply
408
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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
456
views
affymetrix
genomes Annotation
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
467
views
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
replies
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
replies
916
views
ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 14 months ago by • 0
0
votes
0
replies
338
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
13 months ago user_bioinfo • 0
0
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0
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403
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
670
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
607
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
14 months ago Fernanda • 0
0
votes
1
reply
499
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
votes
0
replies
643
views
Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
15 months ago Ragnhild • 0
0
votes
0
replies
665
views
Job: Ensembl Job Vacancies
genomes Annotation GenomicVariation ensembldb
15 months ago Aleena_Ensembl ▴ 30
0
votes
0
replies
939
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
772
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
1.4k
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
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 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
votes
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
votes
0
replies
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
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 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
0
votes
5
replies
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
votes
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
replies
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
2.1k
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
12.3 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 12.6 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
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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…
Votes
C: DESeq2 Following RSEM
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
Awards • All
Popular Question to James W. MacDonald 68k
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