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News: Workshop on Virtual Screening on Drug Discovery from scratch (15-16 September, 2023 : 07.00 - 09.00 PM IST)
workshop virtual-screening
updated 7 weeks ago by 41k • written 11 weeks ago by • 0
0
votes
0
replies
225
views
News: RNAseq data analysis with R/Bioconductor
R RNA-seq Bioconductor
updated 7 weeks ago by 41k • written 11 weeks ago by ★ 2.4k
0
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0
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246
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News: Course - RNAseq in non-model organisms
R Differential-Expression-Analysis RNA-seq Bioconductor
updated 7 weeks ago by 41k • written 11 weeks ago by ★ 2.4k
4
votes
2
replies
394
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News: Standalone NCBI ClusteredNR database now available for download
ClusteredNR NCBI standalone BLAST
12 weeks ago by PeterC_NCBI ▴ 370
0
votes
0
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236
views
News: Virtual Variant Detection Workshop: September 11-14, 2023
tutorial detection genomics workshop variant
12 weeks ago by mia.nahom ▴ 10
0
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0
replies
226
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News: Introduction to Deep Learning for Biologists course
Python Deep-Learning Machine-Learning
updated 12 weeks ago by 41k • written 12 weeks ago by ★ 2.4k
0
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0
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222
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News: Course - Reproducibility Data Analysis with R
R renv Version-Control Reproducibility
updated 7 weeks ago by 41k • written 12 weeks ago by ★ 2.4k
0
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0
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305
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News: Online course: Easily analyze single cell RNA-seq data with Cellenics®, a user-friendly web-based platform
scRNA-seq training single-cell-RNA-seq
updated 12 weeks ago by 41k • written 12 weeks ago by • 0
0
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0
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358
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News: Join Our Online Course: Incorporating Paleogenomes into Evolutionary Genomics Studies
Paleogenomics Genomics aDNA Adaptation-Genomics
updated 12 weeks ago by 41k • written 12 weeks ago by ★ 2.4k
0
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0
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230
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News: Course on Phylogenomics
Phylogenetic-Inference Divergence-Time-Estimation Genomics Phylogenomics
updated 12 weeks ago by 41k • written 12 weeks ago by ★ 2.4k
0
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0
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262
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News: Course. -Multivariate Data Analysis with R and vegan
R vegan MultivariateDataAnalysis
3 months ago by carlopecoraro2 ★ 2.4k
3
votes
2
replies
481
views
News: NCBI BLAST+ 2.14.1 Now Available
NCBI BLAST
3 months ago by PeterC_NCBI ▴ 370
1
vote
0
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214
views
News: Course - Introduction to CRISPR
CRISPR Evolution GenomeEditing
3 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
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224
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News: Upcoming Learning Opportunities and Important Updates
R Programming aDNA Paleogenomics
3 months ago by carlopecoraro2 ★ 2.4k
3
votes
5
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2.0k
views
News: (18 August - "Enzyme Stability Prediction") A free webinar on on-going CAFA5 (Critical Assessment of Functional Annotation of proteins) challenge
gene-ontology CAFA protein
3 months ago by Alexander ▴ 200
0
votes
0
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270
views
News: Spatial Omics course
Spatial-Omics Multiplexed-Image-Analysis
updated 7 weeks ago by 41k • written 3 months ago by ★ 2.4k
1
vote
0
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342
views
News: Generalized Additive Models in R
R GAMs Courses
3 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
replies
233
views
News: NIAID Data Ecosystem Discovery Portal
databases data opendata api
3 months ago by ehaag ▴ 20
0
votes
0
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301
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News: Course - Structural Variant detection and comparison
SVs Structural-Variants
updated 3 months ago by 41k • written 3 months ago by ★ 2.4k
0
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0
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272
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News: course -Developing R/Bioconductor Packages for Genomics
R Genomics Bioconductor
updated 3 months ago by 41k • written 3 months ago by ★ 2.4k
4
votes
3
replies
782
views
News: You may need to cleanup duplicate NCBI BLAST nt database volumes on your system
databases NCBI BLAST
3 months ago by PeterC_NCBI ▴ 370
0
votes
0
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297
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News: Course - Data Visualization in R with ggplot2
R Data-Visualization ggplot2
updated 4 months ago by 41k • written 4 months ago by ★ 2.4k
38
votes
7
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1.9k
views
News: 2 last seats available - 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
Transcriptomics DNA-Seq Variant-Calling RNA-Seq
4 months ago by David Langenberger 10k
9
votes
4
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2.2k
views
7 follow
News: fastp 0.22 released, with new FASTQ deduplication feature.
fastp
updated 4 months ago by 41k • written 2.3 years ago by ★ 2.5k
0
votes
0
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349
views
News: Course - RADseq data analysis with Stacks
RADseq Phylogenomics Stacks Population-genomics
updated 3 months ago by 41k • written 4 months ago by ★ 2.4k
0
votes
0
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301
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News: course - DNA METHYLATION IN ECOLOGY AND EVOLUTION
Non-Model-Organisms DNA-Methylation BS-seq
updated 3 months ago by 41k • written 4 months ago by ★ 2.4k
2
votes
0
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413
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News: Registration open for Nextflow Summit 2023, and free online Nextflow / nf-core training
nextflow
4 months ago by Marcel Ribeiro-Dantas ▴ 450
0
votes
0
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315
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News: 2-day Course on Introduction to Nextflow
Workflow Reproducibility Nextflow
updated 4 months ago by 41k • written 4 months ago by ★ 2.4k
0
votes
0
replies
281
views
News: Physalia courses in September
Genomics R Data-Science
updated 4 months ago by 41k • written 4 months ago by ★ 2.4k
0
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0
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335
views
News: Cellosaurus release 46
knowledgebase cell-line cellosaurus
5 months ago by Amos Bairoch ▴ 110
0
votes
0
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258
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News: Course - Data Manipulation and Visualization in Python
Data-Manipulation Data-Visualisation Python
updated 5 months ago by 41k • written 5 months ago by ★ 2.4k
0
votes
0
replies
401
views
News: Kindle edition of book NO LONGER available. Book available for free
Computational-Biology
5 months ago by sinha.shriprakash ▴ 20
0
votes
0
replies
360
views
News: Course on Generalised Linear Mixed Models in R
GLMM R Statistics Mixed-Models
updated 5 months ago by 41k • written 5 months ago by ★ 2.4k
0
votes
0
replies
359
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
R Systems-Biology Network-Analysis Bioconductor
updated 3 months ago by 41k • written 5 months ago by ★ 2.4k
0
votes
0
replies
264
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News: course on Reproducibility data analysis with R
R Reproducibility Git Github
5 months ago by carlopecoraro2 ★ 2.4k
38
votes
8
replies
1.3k
views
6 follow
News: What happens when a bioinformatician has his own genome sequenced for $300?
DNAseq DNA WGS
updated 5 months ago by 35k • written 5 months ago by 10k
4
votes
0
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456
views
News: A Practical Introduction to Single-Cell RNA-Seq Data Analysis (November 8-10, 2023 in Berlin, Germany)
NGS RNA-Seq single-cell workshop
5 months ago by David Langenberger 10k
0
votes
0
replies
528
views
News: Hands-On NGS Data Analysis Courses 2023
RNA-seq DNA-seq Workshop
updated 5 months ago by 41k • written 5 months ago by 10k
1
vote
0
replies
338
views
News: Course - Introduction to Deep Learning for biologists
Genomics Deep-Learning Python NGS
updated 5 months ago by 41k • written 5 months ago by ★ 2.4k
1
vote
0
replies
344
views
News: Good bioinformatics training resources
NGS
updated 5 months ago by 158k • written 5 months ago by ▴ 70
0
votes
0
replies
407
views
News: Generalized Linear Models (GLM) course in R
R GLM statistics
5 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
replies
380
views
News: course - Advanced Python programming
Python Deep-Learning Machine-Learning
updated 3 months ago by 41k • written 6 months ago by ★ 2.4k
3
votes
2
replies
570
views
News: Participate in a NCBI/NIAID Virtual Codeathon: VCF Files for Population Genomics, Jul 31 - Aug 4, 2023
VCF SARS-CoV-2 NCBI Codeathon
6 months ago by PeterC_NCBI ▴ 370
0
votes
0
replies
295
views
News: Virtual Genome Annotation Workshop
annotation genome workshop
6 months ago by mia.nahom ▴ 10
0
votes
0
replies
518
views
News: Course - Longitudinal data analysis in R
Longitudinal-Data R Genomics
updated 6 months ago by 41k • written 6 months ago by ★ 2.4k
0
votes
0
replies
307
views
News: New version of ElasticBLAST (1.1.0) available from NCBI
ElasticBLAST BLAST. NCBI
6 months ago by PeterC_NCBI ▴ 370
0
votes
0
replies
291
views
News: Course - Introduction to CRISPR for Ecology and Evolution Studies
Genomics CRISPR
6 months ago by carlopecoraro2 ★ 2.4k
0
votes
0
replies
1.2k
views
News: GWAS course
GWAS R
updated 6 months ago by 41k • written 6 months ago by ★ 2.4k
0
votes
0
replies
388
views
News: Course - RNAseq data analysis with R/Bioconductor
R Tidyverse RNA-seq Bioconductor
updated 3 months ago by 41k • written 6 months ago by ★ 2.4k
0
votes
0
replies
354
views
News: Course - Multiplex imagine analysis/ Spatial Omics
Multiplex-Image-Analysis Spatial-Omics
updated 6 months ago by 41k • written 6 months ago by ★ 2.4k
1,000 results • Page 2 of 20
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Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
Extract UMIs using UMI-tools
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Popular Question to O.rka ▴ 710
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Recent Replies
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by dsull ★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM? by rpolicastro 12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks by Ankit ▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by cmdcolin ★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by rpolicastro 12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file by ATpoint 78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by ATpoint 78k
DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
Comment: p-value combination methods by dsull ★ 5.0k
Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by RNAseqer ▴ 250
Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by Nitin Narwade ★ 1.5k
Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
Comment: Construction of single sequence assembly out of contigs by analyst ▴ 10
Thanks colindaven!
Comment: Generate Read counts from bam file by Enrique • 0
Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
Comment: Generate Read counts from bam file by ATpoint 78k
No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
Answer: Generate Read counts from bam file by Enrique • 0
Hello, I recommend you using the mitochondrial reference genome. For the GTF file (or GFF, they are in general the same), checkout this pos…
Comment: How to deeply sequence long inserts by Brian Bushnell 19k
Merging paired reads is a good idea. Then you get nice, long reads... and actually, as long as you have enough coverage, you can just mer…
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