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News: Course - Mass Spectrometry and Proteomics in R/Bioconductor
Bioconductor MassSpectrometry R Proteomics
10 months ago by carlopecoraro2 ★ 2.4k
1
vote
0
replies
513
views
News: Course - Machine Learning in R (for omics data)
Genomics omics MachineLearning R
10 months ago by carlopecoraro2 ★ 2.4k
2
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0
replies
361
views
News: Course - Reproducibility in Bioinformatics
Reproducibility
updated 10 months ago by 41k • written 10 months ago by ★ 2.4k
0
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0
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317
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News: course - Multivariate data analysis with R and vegan
Statistics MultivariateAnalysis R vegan
10 months ago by carlopecoraro2 ★ 2.4k
0
votes
2
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937
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News: Online Course - A Practical Introduction to NGS Data Analysis (February 01-03, 2023)
NGS DNAseq variant-calling RNAseq
10 months ago by David Langenberger 10k
0
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0
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391
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News: Bioinformatics courses in February
Genomics Bioinformatics-Training
updated 6 months ago by 41k • written 10 months ago by ★ 2.4k
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0
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1.1k
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News: Reminder: NCBI Aspera access, update Aspera Connect by Feb 1, 2023
Aspera NCBI SRA GenBank
10 months ago by PeterC_NCBI ▴ 370
1
vote
2
replies
585
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News: Course: Network Analysis in R
NetworkAnalyis R
10 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
replies
400
views
News: de novo RNA-seq Analysis Workshop
virtual workshop rna transcriptome
10 months ago by mia.nahom ▴ 10
0
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0
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537
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News: Genomic Prediction course
Selective-Breeding Genomic-Prediction
updated 10 months ago by 41k • written 10 months ago by ★ 2.4k
1
vote
0
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601
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News: course: Meta-analysis in R
Statistics MetaAnalysis R
10 months ago by carlopecoraro2 ★ 2.4k
0
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0
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476
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News: GSEA in R/Bioconductor course
Bioconductor R GSEA GeneSetEnrichmentAnalysis
10 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
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847
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News: For NCBI Aspera access, update Aspera Connect by Feb 1, 2023
Aspera NCBI GenBank
10 months ago by PeterC_NCBI ▴ 370
0
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0
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402
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News: Metabarcoding in Microbial Ecology
Metabarcoding Qiime2 16S MicrobialEcology R
10 months ago by carlopecoraro2 ★ 2.4k
0
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0
replies
380
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News: Metagenomics tools recommeder system
NGS Metagenomics Recommender-system
updated 10 months ago by 41k • written 10 months ago by • 0
0
votes
0
replies
673
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News: Hands-On NGS Data Analysis Workshops 2023
NGS Workshop RNA-Seq DNA-Seq
11 months ago by David Langenberger 10k
1
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5
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990
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News: Cancer Genomics course - 2 seats left
Genomics Cancer-Genomics R
updated 10 months ago by 41k • written 11 months ago by ★ 2.4k
0
votes
0
replies
390
views
News: Course on Generalised Additive Models In R
Statistics GAMs R
11 months ago by carlopecoraro2 ★ 2.4k
0
votes
1
reply
564
views
News: Sex Chromosome Evolution course
Genomics Sex-Chromosome-Evolution
updated 10 months ago by 41k • written 11 months ago by ★ 2.4k
1
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2
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1.3k
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News: New chat server (Discord) for bioinformatics
community
11 months ago by Samuel Lampa ★ 1.3k
0
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0
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534
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News: Online course - Genome Assembly and Annotation
Long-reads Genome-Annotation Biodiversity Genome-Assembly
updated 10 months ago by 41k • written 11 months ago by ★ 2.4k
1
vote
3
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785
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News: NCBI BLAST ClusteredNR database now available for blastx and PSI-BLAST searches
PSI-BLAST blastx BLAST NCBI ClusteredNR
11 months ago by PeterC_NCBI ▴ 370
0
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0
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518
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News: Winter School in Bioinformatics - last seats available
Genomics Unix RNA-seq docker
updated 10 months ago by 41k • written 11 months ago by ★ 2.4k
0
votes
0
replies
446
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News: Virtual RNA-seq Analysis (Model Organism) Workshop
virtual expression rna-seq analysis workshop
11 months ago by mia.nahom ▴ 10
0
votes
0
replies
464
views
News: Introduction to R Shiny course
WebApplications R RShiny
11 months ago by carlopecoraro2 ★ 2.4k
1
vote
0
replies
507
views
News: New version of ElasticBLAST (1.0.0) available.
NCBI ElasticBLAST BLAST
11 months ago by PeterC_NCBI ▴ 370
0
votes
1
reply
472
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News: Courses in January - still a few seats available
R-Shiny Genomics Unix R
updated 10 months ago by 41k • written 11 months ago by ★ 2.4k
0
votes
0
replies
327
views
News: Sex Chromosome Evolution course
Genomics Sex-Chromosome-Evolution
updated 11 months ago by 41k • written 11 months ago by ★ 2.4k
0
votes
0
replies
410
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News: Cellosaurus release 44 is available
cellosaurus cell-line
updated 11 months ago by 41k • written 11 months ago by ▴ 110
0
votes
0
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355
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News: Introductory video to the Cellosaurus
cellosaurus cell-line
updated 11 months ago by 41k • written 11 months ago by ▴ 110
0
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3
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893
views
News: Nvidia Clara Parabricks is FREE for R&D
nvidia workflow gpu
updated 11 months ago by 2.8k • written 11 months ago by 158k
2
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3
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577
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News: NCBI Comparative Genome Viewer now allows searches for genes across aligned assemblies
Browser NCBI Alignments Genome
11 months ago by PeterC_NCBI ▴ 370
1
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6
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1.0k
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News: Course - FLOW CYTOMETRY ANALYSIS WITH R/BIOCONDUCTOR
Bioconductor FlowCytometry R
updated 10 months ago by ▴ 80 • written 11 months ago by ★ 2.4k
0
votes
0
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293
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News: INTRODUCTION TO ANALYTICAL PALEOBIOLOGY: FOSSIL RECORD BIASES, DIVERSITY, & BIOGEOGRAPHY
Biogeography Paleobiology R
11 months ago by carlopecoraro2 ★ 2.4k
1
vote
0
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317
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News: Analysis of Cancer Genomes Using R and Bioinformatic Tools
Genomics Cancer-Genomics R
updated 12 months ago by 41k • written 12 months ago by ★ 2.4k
0
votes
0
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468
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News: course - GENOME ASSEMBLY USING OXFORD NANOPORE SEQUENCING
Long-reads Assembly Nanopore Genome
12 months ago by carlopecoraro2 ★ 2.4k
0
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0
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298
views
News: Online training - VERSION CONTROL FOR RESEARCHERS
Version Control Git Github
12 months ago by carlopecoraro2 ★ 2.4k
0
votes
1
reply
389
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News: Research Training In NGS Data Analysis
analysis data-analysis
updated 12 months ago by 41k • written 12 months ago by • 0
0
votes
0
replies
407
views
News: Bayesian regression modeling in R course
RegressionModeling Bayesian R
12 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
replies
370
views
News: Genome Assembly and Annotation course
Annotation Nanopore GenomeAssembly Pacbio
12 months ago by carlopecoraro2 ★ 2.4k
3
votes
0
replies
1.1k
views
News: Changes to the default NCBI BLAST nucleotide database (nt). Learn more and provide feedback!
NCBI Databases BLAST
12 months ago by PeterC_NCBI ▴ 370
0
votes
0
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357
views
News: Nextflow online training
Nextflow Workflow Reproducibility
updated 12 months ago by 41k • written 12 months ago by ★ 2.4k
0
votes
2
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1.2k
views
News: :: FINAL CALL :: Next-Generation Sequencing Data Analysis: A Practical Introduction (December 12-14, 2022 in Munich, Germany)
rnaseq dnaseq sequencing ngs workshop
12 months ago by David Langenberger 10k
0
votes
0
replies
430
views
News: The Association for Single Cell Analysis (ASCA)
genomics singlecell metabolomics sequencing proteomics
12 months ago by dnsv.ev • 0
0
votes
0
replies
383
views
News: Deep Learning in Population Genomics and Phylogeography
DeepLearning Phylogeography PopulationGenomics
13 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
replies
381
views
News: Metabarcoding in Microbial Ecology Workshop
Qiime2 R Metabarcoding Microbial-Ecology
13 months ago by carlopecoraro2 ★ 2.4k
1
vote
2
replies
559
views
News: Gene Set Enrichment Analysis in R/Bioconductor
Gene-Set-Enrichment-Analysis R Cancer-Genomics GSEA
13 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
replies
348
views
News: Analysis of RNA sequencing data with R/Bioconductor course.
Bioconductor RNAseq R
13 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
replies
517
views
News: Winter School in Bioinformatics
course workshop
updated 12 months ago by 41k • written 13 months ago by ★ 2.4k
1
vote
0
replies
420
views
News: Introduction to Nextflow
Nextflow
updated 12 months ago by 41k • written 13 months ago by ★ 2.4k
1,000 results • Page 4 of 20
Recent Votes
Comment: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor
A: difference between GSEA and Gene Ontology
Answer: Does the Minion demultiplex when basecalling?
the difference between the positions called by somatic caller (MuTect2) and the position called by germline caller (UnifiedGenotyper)?
A: Extract somatic mutations and germline mutations from variant calling files?
C: visualizing mutational data using Maftools for reference genome hg19
Answer: Ambient RNA removal method that generates whole (integer) counts
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Popular Question to samreen.jasvi • 0
Teacher to h.mon 35k
Scholar to jared.andrews07 ★ 16k
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Recent Replies
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Ram 41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation by alex.zaccaron ▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV by awhale01 • 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts by EK • 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
Yes at 5%.
Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k
Has phiX been spiked in to increase nucleotide diversity.
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