Showing : genomes • reset
0
votes
1
reply
187
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I am having issues with bowtie2_build
genomes bowtiew Index
updated 4 weeks ago by 68k • written 4 weeks ago by • 0
0
votes
1
reply
148
views
affymetrix
genomes Annotation
updated 5 weeks ago by 68k • written 6 weeks ago by • 0
0
votes
1
reply
175
views
Correlation between gene clusters
genomes RNASeqData
written 8 weeks ago by • 0
0
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0
replies
5
views
Spam: <img/src/onerror=alert&#xFEFF;(1337)>
genomes rgu34cprobe
3 months ago <img/src/onerror=alert&#xFEFF;(1337)> 0
2
votes
5
replies
1.1k
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 3 months ago by 68k • written 3 months ago by • 0
0
votes
3
replies
529
views
ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 5 months ago by • 0
0
votes
0
replies
189
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
3 months ago user_bioinfo • 0
0
votes
0
replies
193
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
3 months ago brayas13 • 0
0
votes
1
reply
342
views
probe ID search for SNP (plink)
genomes
updated 4 months ago by 68k • written 4 months ago by • 0
1
vote
6
replies
941
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 4 months ago by ★ 4.7k • written 5 months ago by • 0
0
votes
0
replies
303
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
5 months ago Fernanda • 0
0
votes
1
reply
327
views
For feline genome
genomes Analysisoffelinegenome
updated 5 months ago by 68k • written 5 months ago by • 0
2
votes
5
replies
816
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
5 months ago ronin • 0
0
votes
0
replies
356
views
Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
5 months ago Ragnhild • 0
0
votes
0
replies
384
views
Job: Ensembl Job Vacancies
genomes Annotation GenomicVariation ensembldb
6 months ago Aleena ▴ 30
0
votes
0
replies
688
views
Job: Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics
genomes
16 months ago JP Carter ▴ 40
0
votes
0
replies
705
views
Job: Bioinformatics Research Associate, Genomics and Genetics
genomes Genetics
16 months ago JP Carter ▴ 40
1
vote
1
reply
615
views
MSc student
genomes
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
0
votes
2
replies
3.6k
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
written 3.0 years ago by • 0
0
votes
0
replies
1.1k
views
How to assign custom colour codes for Multiple sequence alignment (MSA)?
Phylogenetics genomes R MultipleSequenceAlignment Bioconductor
3.6 years ago • updated 3.5 years ago K. • 0
1
vote
0
replies
1.7k
views
Job: Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job computational biology genomes pathways machine learning Job
7.4 years ago bulfin.triona ▴ 10
0
votes
0
replies
1.3k
views
How to generate CpG island Unmasked.bed file format for finding CpG island shores and shelves?
bioconductor annotation rtracklayer genomes homo.sapiens
7.7 years ago sivabala76 • 0
0
votes
5
replies
1.9k
views
Extracting all possible annotations between two genomic coordinates
genomes
8.0 years ago KB ▴ 50
0
votes
0
replies
1.3k
views
vizualization of mutations
genomes SNP
8.5 years ago Bogdan ▴ 670
0
votes
0
replies
2.0k
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
8.5 years ago dtlabmskcc • 0
1
vote
1
reply
1.9k
views
GenomeViz
Proteomics genomes Proteomics genomes
updated 9.1 years ago by • 0 • written 20.1 years ago by ▴ 80
0
votes
1
reply
1.4k
views
Request: Add Macaca fascicularis genome to BSgenome
bsgenome genomes
updated 9.8 years ago by 16k • written 9.8 years ago by • 0
0
votes
0
replies
1.8k
views
Job: Harvard Medical School: Postdoctoral Opportunity
genomes Job
10.4 years ago Doe, Aimee ▴ 40
0
votes
8
replies
3.2k
views
Best practices to find intersection among variants
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 10.5 years ago by ★ 1.3k • written 10.5 years ago by ▴ 220
2
votes
3
replies
5.6k
views
Linkage disequilibrium with 1000 Genomes/HapMap
HapMap genomes HapMap genomes
10.6 years ago enricoferrero ▴ 680
0
votes
3
replies
1.8k
views
Elephant shark genome
Biostrings genomes Biostrings genomes
updated 10.9 years ago by 25k • written 10.9 years ago by ★ 13k
0
votes
1
reply
2.3k
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 10.9 years ago by ▴ 570 • written 10.9 years ago by ▴ 220
0
votes
1
reply
1.8k
views
GOseq with ce6
GO Yeast Organism goseq genomes GO Yeast Organism goseq genomes
updated 10.9 years ago by ▴ 320 • written 10.9 years ago by ▴ 50
0
votes
0
replies
1.8k
views
Trying to use BSgenome.Hsapiens.NCBI.GRCh38
Cancer BSgenome BSgenome genomes Cancer BSgenome BSgenome genomes
10.9 years ago Hervé Pagès 16k
0
votes
1
reply
1.9k
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 10.9 years ago by ▴ 570 • written 10.9 years ago by ▴ 220
0
votes
5
replies
2.2k
views
Rsamtools filtering bam file: RE: MEDIPS.createSet error
GO BSgenome BSgenome Rsamtools genomes MEDIPS GO BSgenome BSgenome Rsamtools genomes
updated 10.9 years ago by 25k • written 10.9 years ago by ▴ 220
0
votes
3
replies
2.5k
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
11.1 years ago Guest User ★ 13k
0
votes
1
reply
1.9k
views
makeTranscriptDbFromUCSC() error
genomes genomes
11.1 years ago Chris Cabanski ▴ 30
0
votes
2
replies
2.5k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription HapMap PolyPhen SIFT convert genomes ensemblVEP Transcription HapMap SIFT
updated 11.1 years ago by ★ 6.8k • written 11.2 years ago by ▴ 30
0
votes
1
reply
2.5k
views
Pairwise Alignment on Large Protein Sequence Data Set
Alignment genomes Alignment genomes
updated 11.2 years ago by 16k • written 11.2 years ago by ★ 13k
0
votes
0
replies
1.6k
views
Gviz and Leishmania genomes
rtracklayer genomes Gviz rtracklayer genomes Gviz
11.3 years ago florian.hahne@novartis.com ★ 1.6k
0
votes
0
replies
2.1k
views
Create a sample file /tab delimited file in QuasR
BSgenome convert BSgenome genomes QuasR BSgenome convert BSgenome genomes QuasR
11.3 years ago Michael Stadler ▴ 350
0
votes
1
reply
1.9k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
GO TranscriptDb goseq genomes GO TranscriptDb goseq genomes
updated 11.4 years ago by ★ 7.2k • written 11.4 years ago by ▴ 80
0
votes
1
reply
1.7k
views
Lifting over a bam file with Rsamtools and GenomicRanges
GenomicRanges genomes GenomicRanges genomes
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ★ 13k
0
votes
0
replies
1.3k
views
SnpStats - STRING_ELT() error and Fst
genomes genomes
11.5 years ago Voke AO ▴ 760
0
votes
1
reply
1.5k
views
Working with non-type strain annotation
Proteomics GO genomes Proteomics GO genomes
updated 11.8 years ago by ★ 7.2k • written 11.8 years ago by ▴ 70
0
votes
8
replies
3.7k
views
QuasR: how to use an indexed reference genome?
BSgenome BSgenome genomes QuasR BSgenome BSgenome genomes QuasR
updated 11.8 years ago by ▴ 350 • written 11.8 years ago by ▴ 750
0
votes
2
replies
1.9k
views
QuasR special case alignment
Alignment genomes QuasR Alignment genomes QuasR
updated 11.8 years ago by ▴ 340 • written 11.8 years ago by ▴ 350
0
votes
6
replies
1.9k
views
coverage on very large ReadGappedAlignmentsObject
Coverage genomes Coverage genomes
updated 11.8 years ago by 25k • written 11.8 years ago by ▴ 360
0
votes
1
reply
2.1k
views
Help needed! What wrong with VariantAnnotation and TCGA vcfs
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 340
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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