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News: Beyond beginner R: Advancing your coding skills - September 16-19
AdvancedCoding Programming R
5 hours ago by carlopecoraro2 ★ 2.5k
795
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167
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142k
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109 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 3 months ago by 2.7k • written 7.4 years ago by 100k
0
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145
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News: Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy Python NumPy
updated 2 days ago by 43k • written 2 days ago by • 0
0
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117
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News: Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis Statistics R
updated 2 days ago by 43k • written 2 days ago by ★ 2.5k
0
votes
1
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271
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News: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq variant-calling RNA-seq illumina transcriptomics
2 days ago by David Langenberger 11k
0
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0
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107
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News: Online course: Genome Annotation
Genome-Assembly Genome-Annotation
3 days ago by carlopecoraro2 ★ 2.5k
3
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0
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197
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News: Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy Generative-AI scRNA Machine-Learning
updated 5 days ago by 43k • written 6 days ago by ▴ 60
0
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0
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164
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News: Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis Statistics R
updated 6 days ago by 43k • written 6 days ago by ★ 2.5k
0
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0
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122
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News: hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models GLM R
updated 7 days ago by 43k • written 8 days ago by ★ 2.5k
3
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0
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130
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News: Interested in Spatial Omics?
Bioconductor Spatial-Omics Spatial-Transcriptomics
updated 8 days ago by 43k • written 9 days ago by ★ 2.5k
0
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0
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92
views
News: Online course: DNA methylation
Pacbio Nanopore DnaMethylation Evolution
10 days ago by carlopecoraro2 ★ 2.5k
0
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0
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138
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News: upcoming online statistical courses
Statistics R Data-Analysis
updated 11 days ago by 43k • written 11 days ago by ★ 2.5k
0
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0
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201
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News: Online course: Meta-analysis in R
Meta-Analysis Statistics R
updated 14 days ago by 43k • written 14 days ago by ★ 2.5k
0
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0
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184
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News: Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo Individual-Based-Models Agent-Based-Models
updated 14 days ago by 43k • written 14 days ago by ★ 2.5k
0
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0
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186
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News: Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop RNA-seq nextflow DNA-seq
updated 15 days ago by 43k • written 16 days ago by 11k
0
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0
replies
149
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News: Deadline Approaching: PETs for Public Health Challenge
privacy public-health-challenge
updated 16 days ago by 43k • written 16 days ago by ▴ 380
0
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0
replies
186
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News: Online course: Network Analysis in R
NetworkAnalyis R
18 days ago by carlopecoraro2 ★ 2.5k
0
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0
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192
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News: Online course: Meta-analysis in R
Meta-Analysis R
updated 20 days ago by 43k • written 20 days ago by ★ 2.5k
1
vote
0
replies
135
views
News: Online Live Course: Introduction to Machine Learning in R
Rstats TScourses Rlang Rproject
updated 21 days ago by 43k • written 21 days ago by ▴ 70
2
votes
0
replies
131
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News: Online Course Generalised Additive Mixed Models (GAMM): modelling space-time correlation structures
GAMM Rlang Rstats Rproject
updated 20 days ago by 43k • written 21 days ago by ▴ 70
2
votes
0
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131
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News: Online Course Introduction to Network Analysis and Modelling
Python Network-Analysis
updated 21 days ago by 43k • written 21 days ago by ▴ 70
2
votes
0
replies
120
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News: Course Functional Programming with R
Rstats TScourses Rproject KeepLearning Rlang
22 days ago by Transmitting Science communication ▴ 70
12
votes
2
replies
467
views
News: 8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop RNA-Seq DNA-Seq Illumina
22 days ago by David Langenberger 11k
2
votes
0
replies
124
views
News: Online course: Genome Annotation
Genome-Assembly RNA-seq Genome-Annotation
updated 22 days ago by 43k • written 22 days ago by ★ 2.5k
0
votes
0
replies
125
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News: Online course: Multivariate Data Analysis with R and vegan
Multivariate-Statistics vegan R
updated 23 days ago by 43k • written 24 days ago by ★ 2.5k
1
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0
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182
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News: Landscape Genomics course in Switzerland
LFMM Landscape-Genomics Sambada R Local-Adaptation
4 hours ago by carlopecoraro2 ★ 2.5k
8
votes
2
replies
795
views
News: FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell sequencing
27 days ago by David Langenberger 11k
0
votes
0
replies
151
views
News: Online course: Food Traceability Using Genomic Tools
Nanopore Genomic-Tools Illumina Food-Traceability
updated 28 days ago by 43k • written 29 days ago by ★ 2.5k
0
votes
0
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153
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News: Online course: Eukaryotic Metabarcoding
Metabarcoding Biodiversity R eDNA
4 weeks ago by carlopecoraro2 ★ 2.5k
3
votes
2
replies
603
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News: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Vol…
mathematical-modelling endocrinology ML systems-biology machine-learning
4 weeks ago by Johannes W. Dietrich • 0
0
votes
0
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213
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News: Online course: Reproducibility in Bioinformatics
Singularity Version-Control Docker Containers
updated 4 weeks ago by 43k • written 4 weeks ago by ★ 2.5k
0
votes
0
replies
179
views
News: Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic Bacterial-Genomics Pangenomics
updated 4 weeks ago by 43k • written 4 weeks ago by ★ 2.5k
0
votes
0
replies
170
views
News: Online course: Introduction to GWAS
GWAS Imputation StatisticalPower
5 weeks ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
168
views
News: Online course: Adaptation Genomics
StructuralVariants Selection AdaptationGenomics PopulationStructure
6 weeks ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
158
views
News: Online course: Analysis of Prokaryotic Pangenomes
BacterialGenomics Pangenomics
6 weeks ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
237
views
News: Online course on Genome Assembly and Annotation (1 seat left)
Galaxy GenomeAssembly GenomeAnnotation
6 weeks ago by carlopecoraro2 ★ 2.5k
1
vote
0
replies
173
views
News: NCBI's ClinVar now accepting somatic variation data
variation NCBI somatic-variants ClinVar
6 weeks ago by PeterC_NCBI ▴ 410
1
vote
1
reply
277
views
News: EMBL Course Hands-on course for sample preparation and data analysis in proteomics
EMBLProteomics
updated 7 weeks ago by • 0 • written 12 weeks ago by ▴ 10
1
vote
0
replies
203
views
News: Learn how to create robust bioinformatics pipelines for reproducible and comparable NGS analyses
nextflow pipeline workshop
7 weeks ago by David Langenberger 11k
0
votes
0
replies
158
views
News: Online course: Genome Assembly and Annotation - 3 seats left
Genome-Assembly Galaxy Genome-Annotation
updated 7 weeks ago by 43k • written 7 weeks ago by ★ 2.5k
0
votes
0
replies
158
views
News: Call for abstract: Quest for Orthologs meeting in Montreal
conference phylogeny comparativegenomics orthology evolution
7 weeks ago by sina.majidian ▴ 20
1
vote
0
replies
162
views
News: shournal: A Tool for Bioinformaticians to Boost Research Reproducibility
reproducability terminal bash
8 weeks ago by David Langenberger 11k
1
vote
1
reply
203
views
News: Integrated Genome Browser (IGB) Office Hours
Integrated-Genome-Browser IGB
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
0
votes
0
replies
193
views
News: Online course: Network Analysis in Systems Biology with R/Bioconductor
R RNA-seq Network-Analysis Bioconductor Systems-Biology
updated 8 weeks ago by 43k • written 8 weeks ago by ★ 2.5k
0
votes
0
replies
226
views
News: The 2024 Canadian Bioinformatics Workshops are here!
CBW workshop training
8 weeks ago by bioinformatics.ca • 0
0
votes
0
replies
179
views
News: Live online course Data Manipulation with R Tidyverse, 3 and 5 of April
R manipulation tidyverse data
9 weeks ago by Sole • 0
0
votes
0
replies
202
views
News: Online course: Reproducibility in Bioinformatics
Docker Singularity WorkflowManagementSystems Reproducibility
9 weeks ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
258
views
News: Online course: Genome Assembly Using Oxford Nanopore Sequencing - 4 seats remaining
GenomeAssembly Nanopore longreads
9 weeks ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
238
views
News: Webinar about scRNA-seq cell type prediction
scRNAseq
updated 9 weeks ago by 142k • written 9 weeks ago by • 0
0
votes
0
replies
250
views
News: Online course: Spatial Omics in R/Bioconductor
R Spatial-Omics Bioconductor tidyverse transcriptomics
updated 10 weeks ago by 43k • written 10 weeks ago by ★ 2.5k
1,000 results • Page 1 of 20
Recent Votes
Comment: Bacterial plasmid analysis
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
A: What is the difference between GRCh37 and hs37? And hg19?
A: Decoy In Reference Assembly
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Recent Replies
Answer: How goes gene length effect the number of reads mapped by i.sudbery 19k
See my answer about the what hows and whens of RNA-seq normalisation here: https://www.biostars.org/p/9586553/#9586566
Comment: What purposes can TPM values be used for? by dsull ★ 5.9k
Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
Answer: What purposes can TPM values be used for? by i.sudbery 19k
See my post here for more details on RNA-seq normalisation: https://www.biostars.org/p/9586553/#9586566 In short, TPM normalises for ge…
Comment: Bacterial plasmid analysis by Zamin Iqbal • 0
I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
Comment: Downsampling long-read BAM files by GenoMax 142k
Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement? You could accept (green check mark) this…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by Estevão • 0
Thank you. My budget is around 20 thousand dollars.
Answer: Problem with data downloaded from Short Reads Archive (SRA) by atharvakarkare14 ▴ 20
Prefetch files using sratoolkit **prefetch** command and then use **fasterq-dump**. There you can see the number of reads. For validation, …
Answer: Downsampling long-read BAM files by eesiribloom ▴ 80
random downsampling of bam files is now possible using [rasusa][1] [v1.0.0][2] with the `aln` subcommand [1]: https://github.com/mbh…
Comment: Problem with data downloaded from Short Reads Archive (SRA) by GenoMax 142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA) by ATpoint 82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples by ATpoint 82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes by Mohamed Abderrahmane ▴ 20
In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA) by Begonia_pavonina ▴ 150
Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq by GenoMax 142k
Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA) by ATpoint 82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
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