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122k
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105 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 5 weeks ago by 2.0k • written 6.8 years ago by 98k
0
votes
1
reply
118
views
News: EMBL-EBI virtual course | Introduction to RNA-seq and functional interpretation
RNA-seq
updated 1 day ago by 40k • written 1 day ago by • 0
1
vote
0
replies
113
views
News: Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
nextflow automation pipeline development
1 day ago by David Langenberger 10k
1
vote
0
replies
119
views
News: Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
NCBI Codeathon
2 days ago by PeterC_NCBI ▴ 330
0
votes
0
replies
131
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 2 days ago by 40k • written 2 days ago by 10k
0
votes
0
replies
139
views
News: Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sequence-analysis sars-cov-2 spike-protein
updated 2 days ago by 40k • written 2 days ago by • 0
0
votes
0
replies
123
views
News: Course: Data Manipulation and Visualisation with Python
Python Data-Visualization Data-Manipulation
updated 4 days ago by 40k • written 4 days ago by ★ 2.3k
0
votes
0
replies
131
views
News: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq RNA-seq Workshop
updated 4 days ago by 40k • written 4 days ago by 10k
0
votes
2
replies
553
views
News: The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) Early bird deadline approaching - 20th September
population-genomics radseq stacks
updated 4 days ago by ★ 1.4k • written 5 days ago by ▴ 110
0
votes
0
replies
130
views
News: Course - GLMMs in R
GLMM Mixed-Models
updated 5 days ago by 40k • written 5 days ago by ★ 2.3k
0
votes
0
replies
129
views
News: Introduction to Nextflow (2 seats left)
Nextflow Workflow Reproducibility
updated 5 days ago by 40k • written 5 days ago by ★ 2.3k
0
votes
0
replies
129
views
News: Genomic Prediction course
Bioinformatics GWAS GenomicPrediction
6 days ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
113
views
News: course - Population Genomics Using Ancient DNA Data
Bioinformatics PopulationGenomics Genomics aDNA
6 days ago by carlopecoraro2 ★ 2.3k
3
votes
5
replies
845
views
News: Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl GTF
updated 10 days ago by ▴ 30 • written 10 months ago by ▴ 30
0
votes
0
replies
125
views
News: NCBI ClinVar XML update to accomodate somatic variants
SNP NCBI XML ClinVar
11 days ago by PeterC_NCBI ▴ 330
0
votes
0
replies
102
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 11 days ago by 134k • written 11 days ago by • 0
0
votes
0
replies
109
views
News: RNAseq data analysis with R/Bioconductor
R RNAseq Bioconductor
11 days ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
137
views
News: Course - RNAseq in non-model organisms
R RNAseq DifferentialExpressionAnalysis Bioconductor
14 days ago by carlopecoraro2 ★ 2.3k
4
votes
2
replies
241
views
News: Standalone NCBI ClusteredNR database now available for download
ClusteredNR NCBI standalone BLAST
18 days ago by PeterC_NCBI ▴ 330
0
votes
0
replies
124
views
News: Virtual Variant Detection Workshop: September 11-14, 2023
tutorial detection genomics workshop variant
18 days ago by mia.nahom ▴ 10
0
votes
0
replies
133
views
News: Introduction to Deep Learning for Biologists course
Python Deep-Learning Machine-Learning
updated 18 days ago by 40k • written 18 days ago by ★ 2.3k
0
votes
0
replies
120
views
News: Course - Reproducibility Data Analysis with R
R renv VersionControl Reproducibility
18 days ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
189
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 22 days ago by 40k • written 22 days ago by • 0
0
votes
0
replies
237
views
News: Join Our Online Course: Incorporating Paleogenomes into Evolutionary Genomics Studies
Paleogenomics Genomics aDNA Adaptation-Genomics
updated 23 days ago by 40k • written 23 days ago by ★ 2.3k
0
votes
0
replies
125
views
News: Course on Phylogenomics
Phylogenetic-Inference Divergence-Time-Estimation Genomics Phylogenomics
updated 23 days ago by 40k • written 23 days ago by ★ 2.3k
0
votes
0
replies
157
views
News: Course. -Multivariate Data Analysis with R and vegan
R vegan MultivariateDataAnalysis
27 days ago by carlopecoraro2 ★ 2.3k
2
votes
2
replies
304
views
News: NCBI BLAST+ 2.14.1 Now Available
NCBI BLAST
29 days ago by PeterC_NCBI ▴ 330
1
vote
0
replies
139
views
News: Course - Introduction to CRISPR
CRISPR Evolution GenomeEditing
4 weeks ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
154
views
News: Upcoming Learning Opportunities and Important Updates
R Programming aDNA Paleogenomics
4 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
175
views
News: Spatial Omics course
MultiplexedImageAnalysis SpatialOmics
5 weeks ago by carlopecoraro2 ★ 2.3k
1
vote
0
replies
261
views
News: Generalized Additive Models in R
R GAMs Courses
6 weeks ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
157
views
News: NIAID Data Ecosystem Discovery Portal
databases data opendata api
6 weeks ago by ehaag ▴ 20
0
votes
0
replies
180
views
News: Course - Structural Variant detection and comparison
SVs Structural-Variants
updated 6 weeks ago by 40k • written 6 weeks ago by ★ 2.3k
0
votes
0
replies
197
views
News: course -Developing R/Bioconductor Packages for Genomics
R Genomics Bioconductor
updated 6 weeks ago by 40k • written 6 weeks ago by ★ 2.3k
4
votes
3
replies
625
views
News: You may need to cleanup duplicate NCBI BLAST nt database volumes on your system
databases NCBI BLAST
29 days ago by PeterC_NCBI ▴ 330
0
votes
0
replies
226
views
News: Course - Data Visualization in R with ggplot2
R Data-Visualization ggplot2
updated 7 weeks ago by 40k • written 7 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
266
views
News: Course - RADseq data analysis with Stacks
RADseq Phylogenomics Stacks Population-genomics
updated 6 weeks ago by 40k • written 9 weeks ago by ★ 2.3k
0
votes
0
replies
219
views
News: course - DNA METHYLATION IN ECOLOGY AND EVOLUTION
Non-Model-Organisms DNA-Methylation BS-seq
updated 6 weeks ago by 40k • written 9 weeks ago by ★ 2.3k
2
votes
0
replies
317
views
News: Registration open for Nextflow Summit 2023, and free online Nextflow / nf-core training
nextflow
10 weeks ago by Marcel Ribeiro-Dantas ▴ 440
0
votes
0
replies
242
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
203
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
270
views
News: Cellosaurus release 46
knowledgebase cell-line cellosaurus
12 weeks ago by Amos Bairoch ▴ 110
0
votes
0
replies
193
views
News: Course - Data Manipulation and Visualization in Python
Data-Manipulation Data-Visualisation Python
updated 12 weeks ago by 40k • written 12 weeks ago by ★ 2.3k
0
votes
0
replies
344
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
275
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
0
votes
0
replies
292
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
R Systems-Biology Network-Analysis Bioconductor
updated 6 weeks ago by 40k • written 3 months ago by ★ 2.3k
0
votes
0
replies
196
views
News: course on Reproducibility data analysis with R
R Reproducibility Git Github
3 months ago by carlopecoraro2 ★ 2.3k
1,000 results • Page 1 of 20
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A: What Do Different Bioinformatics Positions Mean?
A: What Do Different Bioinformatics Positions Mean?
Answer: blastn Command Not Found
Answer: Faster way to download PDBe PISA data
Answer: how to download interface generated with PDBe PISA?
Answer: Is it possible to calculate TPM using 10X Genomics public data?
Answer: Ties in reranked list
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Popular Question to smrutimayipanda ▴ 20
Popular Question to Jeremy Leipzig 21k
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Recent Replies
Comment: Dotplot error: subscript out of bound by Xuhao • 0
Got it. Thanks a lot.
Comment: Merging the filename with tsv files for master file by smrutimayipanda ▴ 20
this is the code which I have written: import os import pandas as pd # Get the list of all the orf.tsv files orf_tsv_…
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
There are plenty of variants that don't exist in gnomAD - only 759M SNPs (chr-pos-ref-alt) out of a possible 9B. Your question is a bit con…
Comment: Modify the code to take most abundant reads from a cluster and process it. by Mohd ▴ 40
Hi, Thanks for the help. I am just a beginner and the code was written by someone else, I am trying to modify it for myself. I will try to …
Comment: Hugo_Symbol to Entrez ID by GenoMax 134k
Using `EntrezDirect` ([**LINK**][1]): $ esearch -db gene -query "TSPAN6 [gene] AND human [orgn]" | esummary | xtract -pattern Document…
Comment: Ties in reranked list by Hamza • 0
I had actually accidentally used ranks instead of Entrez gene ids (but switched later to human Ensembl gene ids). However, without your com…
Comment: Hugo_Symbol to Entrez ID by shakyaram079 • 0
Yes sure. These are all gene IDs BZRAP1, C19orf60, TCEB3 and so on.
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I tried the commands you recommended in the bash/command line. When I tried `find "${bam_directory}" -type f -name "*.bam" | xargs samtools…
Comment: Hugo_Symbol to Entrez ID by GenoMax 134k
Can you provide some examples of HUGO ID's you are unable to convert?
Comment: Using STAR aligner to build index of hg38 by GenoMax 134k
GTF file includes gene models/annotation information. You could also use a program like `salmon/kallisto` with just human transcriptome to…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Pierre Lindenbaum 157k
then test each files. find "${bam_directory}" -type f -name "*.bam" | xargs samtools quickcheck file "${reference_gen…
Answer: Ties in reranked list by alserg ▴ 860
The problem here is not the ties, but that your gene IDs in the pathway list (ensemble human genes) does not match the names of the stats v…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I did not use the space between the `-u` flag and the `-o` flag (the blank line) but I did do what you recommended: # Run CuffDiff wit…
Answer: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Pierre Lindenbaum 157k
how about simply trying: ``` cuffdiff -u "${annotation_gtf}" \ -o "${output_directory}" \ -b "${reference_genome}" \ -p "${num_th…
Comment: Using STAR aligner to build index of hg38 by Grace • 0
Yes, I know also need a GTF file. So the GTF file will include RNA information? Thanks for your answer!!
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