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News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 6 weeks ago by 2.0k • written 6.8 years ago by 98k
0
votes
0
replies
75
views
News: New NCBI Datasets APIs to Replace Old Ones
NCBI API Datasets
23 hours ago by PeterC_NCBI ▴ 330
0
votes
1
reply
224
views
News: LAST CALL: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq Workshop RNA-seq
1 day ago by David Langenberger 10k
0
votes
0
replies
103
views
News: RADseq data analysis course
RADseq Phylogenomics Bioinformatics Populationgenomics Stacks
2 days ago by carlopecoraro2 ★ 2.3k
0
votes
1
reply
179
views
News: EMBL-EBI virtual course | Introduction to RNA-seq and functional interpretation
RNA-seq
updated 4 days ago by 40k • written 4 days ago by • 0
1
vote
0
replies
162
views
News: Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
nextflow automation pipeline development
4 days ago by David Langenberger 10k
2
votes
1
reply
213
views
News: Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
NCBI Codeathon
updated 2 days ago by 10k • written 5 days ago by ▴ 330
0
votes
0
replies
159
views
News: Workshop - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)
workshop scRNA-Seq RNA-Seq single-cell
updated 5 days ago by 40k • written 5 days ago by 10k
0
votes
0
replies
154
views
News: Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sequence-analysis sars-cov-2 spike-protein
updated 5 days ago by 40k • written 5 days ago by • 0
0
votes
0
replies
132
views
News: Course: Data Manipulation and Visualisation with Python
Python Data-Visualization Data-Manipulation
updated 7 days ago by 40k • written 7 days ago by ★ 2.3k
0
votes
2
replies
565
views
News: The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) Early bird deadline approaching - 20th September
population-genomics radseq stacks
updated 7 days ago by ★ 1.4k • written 7 days ago by ▴ 110
0
votes
0
replies
137
views
News: Course - GLMMs in R
GLMM Mixed-Models
updated 8 days ago by 40k • written 8 days ago by ★ 2.3k
0
votes
0
replies
137
views
News: Introduction to Nextflow (2 seats left)
Nextflow Workflow Reproducibility
updated 8 days ago by 40k • written 8 days ago by ★ 2.3k
0
votes
0
replies
136
views
News: Genomic Prediction course
Bioinformatics GWAS GenomicPrediction
9 days ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
120
views
News: course - Population Genomics Using Ancient DNA Data
Bioinformatics PopulationGenomics Genomics aDNA
9 days ago by carlopecoraro2 ★ 2.3k
3
votes
5
replies
856
views
News: Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl GTF
updated 13 days ago by ▴ 30 • written 10 months ago by ▴ 30
0
votes
0
replies
133
views
News: NCBI ClinVar XML update to accomodate somatic variants
SNP NCBI XML ClinVar
14 days ago by PeterC_NCBI ▴ 330
0
votes
0
replies
108
views
News: Workshop on Virtual Screening on Drug Discovery from scratch (15-16 September, 2023 : 07.00 - 09.00 PM IST)
bioinformatics screening virtual
updated 14 days ago by 134k • written 14 days ago by • 0
0
votes
0
replies
117
views
News: RNAseq data analysis with R/Bioconductor
R RNAseq Bioconductor
14 days ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
143
views
News: Course - RNAseq in non-model organisms
R RNAseq DifferentialExpressionAnalysis Bioconductor
16 days ago by carlopecoraro2 ★ 2.3k
4
votes
2
replies
254
views
News: Standalone NCBI ClusteredNR database now available for download
ClusteredNR NCBI standalone BLAST
21 days ago by PeterC_NCBI ▴ 330
0
votes
0
replies
129
views
News: Virtual Variant Detection Workshop: September 11-14, 2023
tutorial detection genomics workshop variant
21 days ago by mia.nahom ▴ 10
0
votes
0
replies
141
views
News: Introduction to Deep Learning for Biologists course
Python Deep-Learning Machine-Learning
updated 21 days ago by 40k • written 21 days ago by ★ 2.3k
0
votes
0
replies
126
views
News: Course - Reproducibility Data Analysis with R
R renv VersionControl Reproducibility
21 days ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
196
views
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 25 days ago by 40k • written 25 days ago by • 0
0
votes
0
replies
250
views
News: Join Our Online Course: Incorporating Paleogenomes into Evolutionary Genomics Studies
Paleogenomics Genomics aDNA Adaptation-Genomics
updated 26 days ago by 40k • written 26 days ago by ★ 2.3k
0
votes
0
replies
131
views
News: Course on Phylogenomics
Phylogenetic-Inference Divergence-Time-Estimation Genomics Phylogenomics
updated 25 days ago by 40k • written 26 days ago by ★ 2.3k
0
votes
0
replies
165
views
News: Course. -Multivariate Data Analysis with R and vegan
R vegan MultivariateDataAnalysis
4 weeks ago by carlopecoraro2 ★ 2.3k
2
votes
2
replies
321
views
News: NCBI BLAST+ 2.14.1 Now Available
NCBI BLAST
4 weeks ago by PeterC_NCBI ▴ 330
1
vote
0
replies
144
views
News: Course - Introduction to CRISPR
CRISPR Evolution GenomeEditing
5 weeks ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
161
views
News: Upcoming Learning Opportunities and Important Updates
R Programming aDNA Paleogenomics
5 weeks ago by carlopecoraro2 ★ 2.3k
3
votes
5
replies
1.7k
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
5 weeks ago by Alexander ▴ 200
0
votes
0
replies
181
views
News: Spatial Omics course
MultiplexedImageAnalysis SpatialOmics
6 weeks ago by carlopecoraro2 ★ 2.3k
1
vote
0
replies
266
views
News: Generalized Additive Models in R
R GAMs Courses
6 weeks ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
162
views
News: NIAID Data Ecosystem Discovery Portal
databases data opendata api
7 weeks ago by ehaag ▴ 20
0
votes
0
replies
185
views
News: Course - Structural Variant detection and comparison
SVs Structural-Variants
updated 7 weeks ago by 40k • written 7 weeks ago by ★ 2.3k
0
votes
0
replies
203
views
News: course -Developing R/Bioconductor Packages for Genomics
R Genomics Bioconductor
updated 7 weeks ago by 40k • written 7 weeks ago by ★ 2.3k
4
votes
3
replies
634
views
News: You may need to cleanup duplicate NCBI BLAST nt database volumes on your system
databases NCBI BLAST
4 weeks ago by PeterC_NCBI ▴ 330
0
votes
0
replies
229
views
News: Course - Data Visualization in R with ggplot2
R Data-Visualization ggplot2
updated 8 weeks ago by 40k • written 8 weeks ago by ★ 2.3k
38
votes
7
replies
1.6k
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
8 weeks ago by David Langenberger 10k
9
votes
4
replies
2.1k
views
7 follow
News: fastp 0.22 released, with new FASTQ deduplication feature.
fastp
updated 8 weeks ago by 40k • written 2.1 years ago by ★ 2.4k
0
votes
0
replies
270
views
News: Course - RADseq data analysis with Stacks
RADseq Phylogenomics Stacks Population-genomics
updated 7 weeks ago by 40k • written 9 weeks ago by ★ 2.3k
0
votes
0
replies
223
views
News: course - DNA METHYLATION IN ECOLOGY AND EVOLUTION
Non-Model-Organisms DNA-Methylation BS-seq
updated 7 weeks ago by 40k • written 10 weeks ago by ★ 2.3k
2
votes
0
replies
324
views
News: Registration open for Nextflow Summit 2023, and free online Nextflow / nf-core training
nextflow
11 weeks ago by Marcel Ribeiro-Dantas ▴ 440
0
votes
0
replies
246
views
News: 2-day Course on Introduction to Nextflow
Workflow Reproducibility Nextflow
updated 11 weeks ago by 40k • written 11 weeks ago by ★ 2.3k
0
votes
0
replies
206
views
News: Physalia courses in September
Genomics R Data-Science
updated 11 weeks ago by 40k • written 11 weeks ago by ★ 2.3k
0
votes
0
replies
274
views
News: Cellosaurus release 46
knowledgebase cell-line cellosaurus
12 weeks ago by Amos Bairoch ▴ 110
0
votes
0
replies
198
views
News: Course - Data Manipulation and Visualization in Python
Data-Manipulation Data-Visualisation Python
updated 3 months ago by 40k • written 3 months ago by ★ 2.3k
0
votes
0
replies
348
views
News: Kindle edition of book NO LONGER available. Book available for free
Computational-Biology
3 months ago by sinha.shriprakash ▴ 20
0
votes
0
replies
282
views
News: Course on Generalised Linear Mixed Models in R
GLMM R Statistics Mixed-Models
updated 3 months ago by 40k • written 3 months ago by ★ 2.3k
1,000 results • Page 1 of 20
Recent Votes
Answer: How to plot proportion of cells in each cluster with scanpy?
Comment: How the first sequencing product removed in pair end sequencing
Comment: WGCNA Labeled Heatmap
C: Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
Comment: Hisat2 index and alignment question
A: Finding overlaps between GRanges objects
A: Finding overlaps between GRanges objects
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Recent Replies
Comment: How to plot proportion of cells in each cluster with scanpy? by bioinfo ▴ 110
Thank you for replying again. The "type" still causes issues but the reply by Radu Tanasa worked.
Comment: How to plot proportion of cells in each cluster with scanpy? by bioinfo ▴ 110
Thank you so much. That worked perfectly and it was much faster than what I was trying.
Answer: Violin plot (Monocle 3) - Troubleshooting by seattlescientist_01 • 0
I'm still stuck on how to fix this.
Answer: How to plot proportion of cells in each cluster with scanpy? by Radu Tanasa ▴ 60
Hi. If I get this right, you simply need to compute the percentage of cells in each cluster at the dataset level? ```py import pandas as p…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by ATpoint 76k
Why would that be an advantage?
Comment: How to plot proportion of cells in each cluster with scanpy? by bk11 ★ 1.2k
The following code will write percentage in your stacked barplot. cross_tab = pd.crosstab(adata.obs['leiden_0.6'],adata.obs['typ…
Comment: How to check RNAseq support for annotated genes? by BioinfoBee • 0
@juke34 Thanks for the suggestion. I wonder if bedtool coverage or intersect can be used to check the transcript support or coverage for ea…
Comment: How to plot proportion of cells in each cluster with scanpy? by bioinfo ▴ 110
Because that was the code from the link. It is how they specified they had 2 groups of samples but I don't have 2 groups. Sorry for the con…
Comment: Violin plot (Monocle 3) - Troubleshooting by bk11 ★ 1.2k
No there is no bug in this. Please see carefully what the `error` message tells to you.
Comment: How to check RNAseq support for annotated genes? by BioinfoBee • 0
@michaeld Thanks. I tried it using STAR to map the transcript to the annotation gtf file, and was planning to use featureCounts/gene Counts…
Comment: How to plot proportion of cells in each cluster with scanpy? by bk11 ★ 1.2k
Why you had `type` in your code above then?
Comment: Comparing multiple columns from two files using AWK by Ram 40k
R's dplyr will serve well here. ```r fileA %>% mutate(V3 = sub(V3, "chr","") %>% inner_join(fileB, join_by(V3 == chr, window_end <= V4, ..…
Comment: How to plot proportion of cells in each cluster with scanpy? by bioinfo ▴ 110
Thank you for the suggestion. Unfortunately, that does not work for me because I do not have a "type" argument in the adata.obs. I think th…
Comment: Violin plot (Monocle 3) - Troubleshooting by seattlescientist_01 • 0
I'm still seeing errors: First I tried the code you mentioned except I use `clusters` instead of `embryo.time.bin` since this is a column…
Comment: Comparing multiple columns from two files using AWK by emiliomastriani ▴ 30
Thank you for the formatting support. Please, can you suggest the code (R/Python) to approach my problem? Something I can use as a starting…
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