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0
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1
reply
450
views
I am having issues with bowtie2_build
genomes bowtiew Index
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
490
views
affymetrix
genomes Annotation
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
1
reply
521
views
Correlation between gene clusters
genomes RNASeqData
written 12 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
14 months ago <img/src/onerror=alert&#xFEFF;(1337)> 0
2
votes
5
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2.3k
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 14 months ago by 68k • written 14 months ago by • 0
0
votes
3
replies
952
views
ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 16 months ago by • 0
0
votes
0
replies
374
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
14 months ago user_bioinfo • 0
0
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0
replies
422
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
14 months ago brayas13 • 0
0
votes
1
reply
704
views
probe ID search for SNP (plink)
genomes
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
6
replies
2.0k
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 15 months ago by ★ 5.0k • written 16 months ago by • 0
0
votes
0
replies
642
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
16 months ago Fernanda • 0
0
votes
1
reply
517
views
For feline genome
genomes Analysisoffelinegenome
updated 16 months ago by 68k • written 16 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
16 months ago ronin • 0
0
votes
0
replies
685
views
Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
16 months ago Ragnhild • 0
0
votes
0
replies
700
views
Job: Ensembl Job Vacancies
genomes Annotation GenomicVariation ensembldb
16 months ago Aleena_Ensembl ▴ 30
0
votes
0
replies
961
views
Job: Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics
genomes
2.2 years ago JP Cartailler ▴ 40
0
votes
0
replies
1.4k
views
Job: Bioinformatics Research Associate, Genomics and Genetics
genomes Genetics
2.2 years ago JP Cartailler ▴ 40
1
vote
1
reply
797
views
MSc student
genomes
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
0
votes
2
replies
4.3k
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
written 3.9 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
4.4 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
8.2 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
8.6 years ago sivabala76 • 0
0
votes
5
replies
2.3k
views
Extracting all possible annotations between two genomic coordinates
genomes
8.9 years ago KB ▴ 50
0
votes
0
replies
1.4k
views
vizualization of mutations
genomes SNP
9.3 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
9.4 years ago dtlabmskcc • 0
1
vote
1
reply
2.0k
views
GenomeViz
Proteomics genomes Proteomics genomes
updated 9.9 years ago by • 0 • written 21.0 years ago by ▴ 80
0
votes
1
reply
1.6k
views
Request: Add Macaca fascicularis genome to BSgenome
bsgenome genomes
updated 10.6 years ago by 16k • written 10.7 years ago by • 0
0
votes
0
replies
2.0k
views
Job: Harvard Medical School: Postdoctoral Opportunity
genomes Job
11.3 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 11.4 years ago by ★ 1.3k • written 11.4 years ago by ▴ 220
2
votes
3
replies
6.2k
views
Linkage disequilibrium with 1000 Genomes/HapMap
HapMap genomes HapMap genomes
11.5 years ago enricoferrero ▴ 680
0
votes
3
replies
2.1k
views
Elephant shark genome
Biostrings genomes Biostrings genomes
updated 11.7 years ago by 25k • written 11.7 years ago by ★ 13k
0
votes
1
reply
2.5k
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 11.8 years ago by ▴ 570 • written 11.8 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 11.8 years ago by ▴ 320 • written 11.8 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
11.8 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 11.8 years ago by ▴ 570 • written 11.8 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 11.8 years ago by 25k • written 11.8 years ago by ▴ 220
0
votes
3
replies
2.8k
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
12.0 years ago Guest User ★ 13k
0
votes
1
reply
2.1k
views
makeTranscriptDbFromUCSC() error
genomes genomes
12.0 years ago Chris Cabanski ▴ 30
0
votes
2
replies
3.0k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription HapMap PolyPhen SIFT convert genomes ensemblVEP Transcription HapMap SIFT
updated 12.0 years ago by ★ 6.8k • written 12.0 years ago by ▴ 30
0
votes
1
reply
2.7k
views
Pairwise Alignment on Large Protein Sequence Data Set
Alignment genomes Alignment genomes
updated 12.1 years ago by 16k • written 12.1 years ago by ★ 13k
0
votes
0
replies
1.9k
views
Gviz and Leishmania genomes
rtracklayer genomes Gviz rtracklayer genomes Gviz
12.2 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
12.2 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 12.2 years ago by ★ 7.2k • written 12.2 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 12.3 years ago by ★ 11k • written 12.3 years ago by ★ 13k
0
votes
0
replies
1.5k
views
SnpStats - STRING_ELT() error and Fst
genomes genomes
12.4 years ago Voke AO ▴ 760
0
votes
1
reply
1.7k
views
Working with non-type strain annotation
Proteomics GO genomes Proteomics GO genomes
updated 12.7 years ago by ★ 7.2k • written 12.7 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 12.7 years ago by ▴ 350 • written 12.7 years ago by ▴ 750
0
votes
2
replies
2.1k
views
QuasR special case alignment
Alignment genomes QuasR Alignment genomes QuasR
updated 12.7 years ago by ▴ 340 • written 12.7 years ago by ▴ 350
0
votes
6
replies
2.2k
views
coverage on very large ReadGappedAlignmentsObject
Coverage genomes Coverage genomes
updated 12.7 years ago by 25k • written 12.7 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 12.8 years ago by 25k • written 12.8 years ago by ▴ 340
115 results • Page 1 of 3
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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