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News: Call for abstract: Quest for Orthologs meeting in Montreal
conference phylogeny comparativegenomics orthology evolution
9 weeks ago by sina.majidian ▴ 20
1
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179
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News: shournal: A Tool for Bioinformaticians to Boost Research Reproducibility
reproducability terminal bash
10 weeks ago by David Langenberger 11k
1
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230
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News: Integrated Genome Browser (IGB) Office Hours
Integrated-Genome-Browser IGB
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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214
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News: Online course: Network Analysis in Systems Biology with R/Bioconductor
R RNA-seq Network-Analysis Bioconductor Systems-Biology
updated 10 weeks ago by 43k • written 10 weeks ago by ★ 2.5k
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244
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News: The 2024 Canadian Bioinformatics Workshops are here!
CBW workshop training
11 weeks ago by bioinformatics.ca • 0
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193
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News: Live online course Data Manipulation with R Tidyverse, 3 and 5 of April
R manipulation tidyverse data
11 weeks ago by Sole • 0
0
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217
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News: Online course: Reproducibility in Bioinformatics
Docker Singularity WorkflowManagementSystems Reproducibility
11 weeks ago by carlopecoraro2 ★ 2.5k
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281
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News: Online course: Genome Assembly Using Oxford Nanopore Sequencing - 4 seats remaining
GenomeAssembly Nanopore longreads
11 weeks ago by carlopecoraro2 ★ 2.5k
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256
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News: Webinar about scRNA-seq cell type prediction
scRNAseq
updated 11 weeks ago by 142k • written 12 weeks ago by • 0
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0
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279
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News: Online course: Spatial Omics in R/Bioconductor
R Spatial-Omics Bioconductor tidyverse transcriptomics
updated 12 weeks ago by 43k • written 12 weeks ago by ★ 2.5k
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230
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News: Online course: Model-Based Demographic Inference from Population Genomics
Demographic-Inference Population-Genomics Demographic-Models
updated 12 weeks ago by 43k • written 12 weeks ago by ★ 2.5k
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209
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News: Online course: R/Bioconductor for Mass Spectrometry and Proteomics
R Proteomics Bioconductor Mass-Spectrometry
updated 3 months ago by 43k • written 3 months ago by ★ 2.5k
0
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212
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News: Virtual Workshops with the UConn Computational Biology Core
Workshop genomics
updated 3 months ago by 142k • written 3 months ago by ▴ 10
0
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0
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198
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News: NGS Data Analysis Courses for Absolute Beginners
NGS DNAseq RNAseq singlecellsequencing DataAnalysis
3 months ago by David Langenberger 11k
0
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212
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News: Online course: Genome Assembly and Annotation
Annotation Genome-Assembly Nanopore Pacbio
updated 3 months ago by 43k • written 3 months ago by ★ 2.5k
0
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0
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195
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News: Online course: Computation Tumor Evolution
R Cancer-Genomics Tumor-Evolution Genomics
updated 3 months ago by 43k • written 3 months ago by ★ 2.5k
0
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0
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193
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News: Course live online Intro Bayesian Analyses, March 4-8, 2024
R python bayesian
3 months ago by Sole • 0
0
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1
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984
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News: FINAL CALL: RNA-Seq Data Analysis Workshop (March 11 - 14, 2024 in Berlin, Germany)
NGS RNA-Seq Workshop
3 months ago by David Langenberger 11k
0
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0
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242
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News: Online course : Meta-Analysis in R
R Meta-Analysis Statistics
updated 3 months ago by 43k • written 3 months ago by ★ 2.5k
1
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208
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News: Cellosaurus release 48 is available
cell-line biocuration cellosaurus knowledgebase
3 months ago by Amos Bairoch ▴ 120
0
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0
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242
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News: Online course: Genome Assembly Using Oxford Nanopore Sequencing
Genome-Assembly Nanopore
updated 3 months ago by 43k • written 3 months ago by ★ 2.5k
0
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0
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266
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News: BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024
NCBI BLAST
3 months ago by PeterC_NCBI ▴ 410
0
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249
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News: EMBL-EBI Training | Systems biology: from large datasets to biological insight
systems
3 months ago by EMBL Events ▴ 10
0
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0
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218
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News: Online course - Sex Chromosome Evolution
Evolution Genomics Sex-Chromosome
updated 3 months ago by 43k • written 3 months ago by ★ 2.5k
0
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1
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833
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News: LAST CALL: Online Course - A Practical Introduction to NGS Data Analysis (February 28 - March 1, 2024)
NGS Online-Workshop
updated 4 months ago by 43k • written 4 months ago by 11k
7
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2
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1.2k
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News: NGS Data Analysis Workshops 2024
scRNA-seq dna-seq rna-seq nextflow
4 months ago by David Langenberger 11k
0
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0
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252
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News: Online course: Generalized Additive Models (GAMs) in R
R Statistics Gams
4 months ago by carlopecoraro2 ★ 2.5k
0
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0
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279
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News: Online course - Introduction to Python for biologists
Python Programming NGSData
4 months ago by carlopecoraro2 ★ 2.5k
1
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0
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218
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News: Online course - Introduction to Machine Learning in R for omics data
R Omics MachineLearning StatisticalLearning
4 months ago by carlopecoraro2 ★ 2.5k
0
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0
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208
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News: Online course - Flow cytometry data analysis with R/Bioconductor
R Flow-Cytometry Bioconductor
updated 4 months ago by 43k • written 4 months ago by ★ 2.5k
0
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1
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341
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News: Reminder: NCBI ClinVar XML update to accommodate somatic variants coming Jan 29, 2024
SNP XML ClinVar NCBI
4 months ago by PeterC_NCBI ▴ 410
4
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0
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221
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News: Transform Your Research with Our NGS Data Analysis Online Course!
DNAseq NGS Biologists OnlineCourse RNAseq
4 months ago by David Langenberger 11k
0
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0
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265
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News: 3rd edition of the Winter School in Bioinformatics - Online February 26 - March 1
genomics reproducibility phylogenomics transcriptomics
4 months ago by carlopecoraro2 ★ 2.5k
0
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0
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587
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News: course - Reproducibility in Bioinformatics
Docker Reproducibility
written 14 months ago by ★ 2.5k
0
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1
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396
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News: Online Course - Genomic Prediction
Genomic-Prediction Selective-Breeding
updated 4 months ago by 43k • written 4 months ago by ★ 2.5k
0
votes
0
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290
views
News: Flow cytometry data analysis with R/Bioconductor course
FlowCytometry R Bioconductor
4 months ago by carlopecoraro2 ★ 2.5k
2
votes
2
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549
views
News: Unix and Shell Scripting for Bioinformatics course
Bash Unix Shell-Scripting
5 months ago by carlopecoraro2 ★ 2.5k
0
votes
0
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337
views
News: Bayesian Data Analysis in R course
R Bayesian-Statistics
updated 5 months ago by 43k • written 5 months ago by ★ 2.5k
0
votes
0
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346
views
News: Practical Hands-On Introduction to R course
R Tidyverse Data-Analysis
updated 5 months ago by 43k • written 5 months ago by ★ 2.5k
0
votes
0
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309
views
News: Landscape Genomics course at the EPFL in Lausanne, Switzerland
genomics Landscape-Genomics
updated 5 months ago by 43k • written 5 months ago by ★ 2.5k
0
votes
0
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296
views
News: New version of ElasticBLAST (1.2.0) available from NCBI
ElasticBLAST NCBI BLAST
5 months ago by PeterC_NCBI ▴ 410
0
votes
0
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290
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News: Course. - Gene Set Enrichment Analysis in R/Bioconductor - ONLINE, 22-25 January
R Gene-Set-Enrichment-Analysis GSEA Bioconductor
updated 5 months ago by 43k • written 5 months ago by ★ 2.5k
0
votes
0
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309
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News: University of Connecticut Single Cell RNA-seq Workshop December 12-15, 2023
expression singlecell rnaseq
5 months ago by mia.nahom ▴ 10
0
votes
0
replies
287
views
News: Online course: Introduction to Python, February 12th-March 11th, 2024
python courses
5 months ago by Sole • 0
0
votes
1
reply
393
views
News: Course: Genome Assembly and Annotation
Biodiversity Genome-Assembly Genome-Annotation Long-reads
updated 5 months ago by 43k • written 5 months ago by ★ 2.5k
0
votes
0
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360
views
News: GWAS course
R GWAS
updated 5 months ago by 43k • written 5 months ago by ★ 2.5k
3
votes
0
replies
312
views
News: NCBI BLAST+ 2.2.15 now available for download
NCBI Taxonomy BLAST
5 months ago by PeterC_NCBI ▴ 410
0
votes
0
replies
317
views
News: Course - Introduction to R Shiny
R Data-Visualisation Shiny
updated 5 months ago by 43k • written 5 months ago by ★ 2.5k
0
votes
0
replies
288
views
News: Online expert taught RNA-Seq workshop
workshop
5 months ago by fturner ▴ 10
0
votes
0
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332
views
News: Course - RNAseq in non-model organisms
Pacbio RNA-seq Nanopore
updated 5 months ago by 43k • written 5 months ago by ★ 2.5k
1,000 results • Page 2 of 20
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index by Lorenzo • 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED? by dthorbur ★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto by dariober 14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err by GenoMax 142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
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