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News: The Biostar Handbook. A bioinformatics e-book for beginners.
training tutorial News handbook
updated 4 months ago by 1.5k • written 6.1 years ago by 96k
0
votes
0
replies
157
views
News: Course - Machine Learning in R (for omics data)
Genomics omics MachineLearning R
23 hours ago by carlopecoraro2 ★ 2.2k
2
votes
0
replies
115
views
News: Course - Reproducibility in Bioinformatics
Bioinformatics Reproducibility
1 day ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
77
views
News: course - Multivariate data analysis with R and vegan
Statistics MultivariateAnalysis R vegan
3 days ago by carlopecoraro2 ★ 2.2k
0
votes
2
replies
503
views
News: Online Course - A Practical Introduction to NGS Data Analysis (February 01-03, 2023)
NGS DNAseq variant-calling RNAseq
5 days ago by David Langenberger 9.8k
0
votes
0
replies
146
views
News: Bioinformatics courses in February
Genomics BioinformaticsTraining
2 days ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
78
views
News: Reminder: NCBI Aspera access, update Aspera Connect by Feb 1, 2023
Aspera NCBI SRA GenBank
5 days ago by PeterC_NCBI ▴ 180
1
vote
2
replies
232
views
News: Course: Network Analysis in R
NetworkAnalyis R
6 days ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
137
views
News: de novo RNA-seq Analysis Workshop
virtual workshop rna transcriptome
9 days ago by mia.nahom • 0
0
votes
0
replies
147
views
News: Genomic Prediction course
Bioinformatics SelectiveBreeding GenomicPrediction
12 days ago by carlopecoraro2 ★ 2.2k
1
vote
0
replies
215
views
News: course: Meta-analysis in R
Statistics MetaAnalysis R
13 days ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
224
views
News: GSEA in R/Bioconductor course
Bioconductor R GSEA GeneSetEnrichmentAnalysis
14 days ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
132
views
News: For NCBI Aspera access, update Aspera Connect by Feb 1, 2023
Aspera NCBI GenBank
15 days ago by PeterC_NCBI ▴ 180
0
votes
0
replies
189
views
News: Metabarcoding in Microbial Ecology
Metabarcoding Qiime2 16S MicrobialEcology R
15 days ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
182
views
News: Metagenomics tools recommeder system
NGS Metagenomics Recommender-system
updated 15 days ago by 37k • written 16 days ago by • 0
0
votes
0
replies
164
views
News: Hands-On NGS Data Analysis Workshops 2023
NGS Workshop RNA-Seq DNA-Seq
19 days ago by David Langenberger 9.8k
1
vote
5
replies
542
views
News: Cancer Genomics course - 2 seats left
CancerGenomics Genomics R Bioinformatics
updated 18 days ago by ★ 2.2k • written 21 days ago by ★ 2.2k
0
votes
0
replies
163
views
News: Course on Generalised Additive Models In R
Statistics GAMs R
20 days ago by carlopecoraro2 ★ 2.2k
0
votes
1
reply
336
views
News: Sex Chromosome Evolution course
Bioinformatics Genomics SexChromosomeEvolution
updated 21 days ago by ▴ 10 • written 21 days ago by ★ 2.2k
1
vote
2
replies
385
views
News: New chat server (Discord) for bioinformatics
community
20 days ago by Samuel Lampa ★ 1.3k
0
votes
0
replies
196
views
News: Online course - Genome Assembly and Annotation
Longreads Bioinformatics GenomeAnnotation Biodiversity GenomeAssembly
22 days ago by carlopecoraro2 ★ 2.2k
0
votes
3
replies
400
views
News: NCBI BLAST ClusteredNR database now available for blastx and PSI-BLAST searches
PSI-BLAST blastx BLAST NCBI ClusteredNR
23 days ago by PeterC_NCBI ▴ 180
1
vote
0
replies
481
views
News: New ebook: From cell line to Command line to learn computational biology
snakemake biology unix RNAseq computational
4 weeks ago by Ming Tang ★ 2.9k
0
votes
0
replies
297
views
News: Winter School in Bioinformatics - last seats available
docker Bioinformatics RNAseq Unix Genomics
4 weeks ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
197
views
News: Virtual RNA-seq Analysis (Model Organism) Workshop
virtual expression rna-seq analysis workshop
4 weeks ago by mia.nahom • 0
0
votes
0
replies
225
views
News: Introduction to R Shiny course
WebApplications R RShiny
5 weeks ago by carlopecoraro2 ★ 2.2k
1
vote
0
replies
256
views
News: New version of ElasticBLAST (1.0.0) available.
NCBI ElasticBLAST BLAST
5 weeks ago by PeterC_NCBI ▴ 180
0
votes
1
reply
248
views
News: Courses in January - still a few seats available
Bioinformatics Unix RShiny Genomics R
updated 5 weeks ago by ▴ 10 • written 5 weeks ago by ★ 2.2k
0
votes
0
replies
146
views
News: Sex Chromosome Evolution course
Genomics Sex-Chromosome-Evolution
updated 5 weeks ago by 37k • written 5 weeks ago by ★ 2.2k
0
votes
0
replies
188
views
News: Cellosaurus release 44 is available
cellosaurus cell-line
updated 6 weeks ago by 37k • written 6 weeks ago by ▴ 110
0
votes
0
replies
167
views
News: Introductory video to the Cellosaurus
cellosaurus cell-line
updated 6 weeks ago by 37k • written 6 weeks ago by ▴ 110
0
votes
3
replies
367
views
News: Nvidia Clara Parabricks is FREE for R&D
nvidia workflow gpu
updated 6 weeks ago by 2.6k • written 6 weeks ago by 152k
2
votes
3
replies
271
views
News: NCBI Comparative Genome Viewer now allows searches for genes across aligned assemblies
Browser NCBI Alignments Genome
6 weeks ago by PeterC_NCBI ▴ 180
1
vote
6
replies
541
views
News: Course - FLOW CYTOMETRY ANALYSIS WITH R/BIOCONDUCTOR
Bioconductor FlowCytometry R
updated 15 days ago by ▴ 70 • written 6 weeks ago by ★ 2.2k
0
votes
0
replies
127
views
News: INTRODUCTION TO ANALYTICAL PALEOBIOLOGY: FOSSIL RECORD BIASES, DIVERSITY, & BIOGEOGRAPHY
Biogeography Paleobiology R
6 weeks ago by carlopecoraro2 ★ 2.2k
1
vote
0
replies
153
views
News: Analysis of Cancer Genomes Using R and Bioinformatic Tools
Genomics Cancer-Genomics R
updated 7 weeks ago by 37k • written 7 weeks ago by ★ 2.2k
0
votes
0
replies
229
views
News: course - GENOME ASSEMBLY USING OXFORD NANOPORE SEQUENCING
Long-reads Assembly Nanopore Genome
7 weeks ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
121
views
News: Online training - VERSION CONTROL FOR RESEARCHERS
Version Control Git Github
7 weeks ago by carlopecoraro2 ★ 2.2k
0
votes
1
reply
193
views
News: Research Training In NGS Data Analysis
analysis data-analysis
updated 8 weeks ago by 37k • written 8 weeks ago by • 0
0
votes
0
replies
234
views
News: Bayesian regression modeling in R course
RegressionModeling Bayesian R
9 weeks ago by carlopecoraro2 ★ 2.2k
0
votes
4
replies
361
views
News: Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl GTF
updated 6 weeks ago by ★ 2.1k • written 9 weeks ago by ▴ 10
0
votes
0
replies
176
views
News: Genome Assembly and Annotation course
Annotation Nanopore GenomeAssembly Pacbio
9 weeks ago by carlopecoraro2 ★ 2.2k
3
votes
0
replies
743
views
News: Changes to the default NCBI BLAST nucleotide database (nt). Learn more and provide feedback!
NCBI Databases BLAST
10 weeks ago by PeterC_NCBI ▴ 180
0
votes
0
replies
191
views
News: Nextflow online training
Nextflow Workflow Reproducibility
updated 7 weeks ago by 37k • written 10 weeks ago by ★ 2.2k
0
votes
2
replies
866
views
News: :: FINAL CALL :: Next-Generation Sequencing Data Analysis: A Practical Introduction (December 12-14, 2022 in Munich, Germany)
rnaseq dnaseq sequencing ngs workshop
10 weeks ago by David Langenberger 9.8k
0
votes
0
replies
222
views
News: The Association for Single Cell Analysis (ASCA)
genomics singlecell metabolomics sequencing proteomics
10 weeks ago by dnsv.ev • 0
0
votes
0
replies
162
views
News: Deep Learning in Population Genomics and Phylogeography
DeepLearning Phylogeography PopulationGenomics
11 weeks ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
186
views
News: Metabarcoding in Microbial Ecology Workshop
Qiime2 R Metabarcoding Microbial-Ecology
12 weeks ago by carlopecoraro2 ★ 2.2k
1
vote
2
replies
282
views
News: Gene Set Enrichment Analysis in R/Bioconductor
Gene-Set-Enrichment-Analysis R Cancer-Genomics GSEA
12 weeks ago by carlopecoraro2 ★ 2.2k
0
votes
0
replies
187
views
News: Analysis of RNA sequencing data with R/Bioconductor course.
Bioconductor RNAseq R
12 weeks ago by carlopecoraro2 ★ 2.2k
1,000 results • Page 1 of 20
Recent Votes
A: Using ColSums vs sizeFactors in read count normalization
Comment: a problem with getBM
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
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Teacher to ATpoint 68k
Popular Question to tianshenbio ▴ 160
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Recent Replies
Answer: how to do a reliable single cell sequencing analysis? by ATpoint 68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM by sanaz • 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v by fuellen ▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM by Mike Smith ★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome by congliu37 • 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File? by Jeremy Leipzig 21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)? by Fabio Marroni ★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism by Rob ▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers by Pierre Lindenbaum 152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence by vvasta • 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation? by Fabio Marroni ★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2 by Fabio Marroni ★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file** by Pierre Lindenbaum 152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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