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News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 3 months ago by 2.8k • written 7.4 years ago by 100k
122
votes
44
replies
11k
views
24 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 6 months ago by 43k • written 11.5 years ago by 100k
24
votes
21
replies
7.6k
views
9 follow
News: Misunderstood parameter of NCBI BLAST
blast alignment
updated 11 months ago by 43k • written 5.6 years ago by ★ 3.4k
6
votes
13
replies
2.1k
views
News: Ensembl reduced functionality: 10th March-16th April 2020
BLAT VEP Ensembl service
updated 11 months ago by 43k • written 4.2 years ago by ★ 2.4k
11
votes
11
replies
1.8k
views
8 follow
News: Python Data Visualization Course. Last 3 spots left
next-gen
updated 11 months ago by 43k • written 5.5 years ago by ★ 2.5k
14
votes
11
replies
3.0k
views
6 follow
News: Announcing bioSyntax: Syntax highlighting for biological files
computational-biology
updated 12 months ago by 43k • written 6.4 years ago by ▴ 170
13
votes
9
replies
2.7k
views
7 follow
News: Inviting NEW Biostars moderators to join Biostars slack channel
slack moderator
7 months ago by GenoMax 142k
38
votes
8
replies
1.7k
views
6 follow
News: What happens when a bioinformatician has his own genome sequenced for $300?
DNAseq DNA WGS
updated 11 months ago by 35k • written 11 months ago by 11k
8
votes
8
replies
2.9k
views
News: Coronavirus Genome Analysis: a new volume in the Biostar Handbook
biostar-handbook education
updated 11 months ago by 43k • written 4.2 years ago by 100k
2
votes
7
replies
1.7k
views
News: Bioinformatics workshop or training courses
RNA-Seq next-gen ChIP-Seq
updated 11 months ago by 43k • written 5.8 years ago by ▴ 140
6
votes
7
replies
2.3k
views
News: NCBI wants to remove quality scores from SRA
quality-scores trimming Assembly genome SRA
updated 11 months ago by 43k • written 3.9 years ago by ▴ 40
38
votes
7
replies
2.3k
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
9 months ago by David Langenberger 11k
2
votes
7
replies
1.8k
views
News: Beyond pest control: What can we learn from parasites?
docking heme parasitism in-silico
updated 11 months ago by 43k • written 5.2 years ago by 54k
8
votes
6
replies
1.5k
views
News: Illumina to Acquire Pacific Biosciences
pacbio illumina
updated 11 months ago by 43k • written 5.5 years ago by 100k
3
votes
5
replies
2.3k
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
9 months ago by Alexander ▴ 220
3
votes
5
replies
1.3k
views
News: Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl GTF
updated 8 months ago by ▴ 120 • written 18 months ago by ▴ 30
0
votes
5
replies
1.6k
views
News: LAST CALL - 'Introduction to NGS Data Analysis' course in Berlin, October 8-10 2018
NGS training RNA-Seq DNA-Seq
updated 11 months ago by 43k • written 5.9 years ago by 11k
1
vote
4
replies
2.0k
views
News: webserver of TCGA data www.tcgaportal.org
genome RNA-Seq TCGA gene
updated 11 months ago by 43k • written 6.0 years ago by ▴ 40
8
votes
4
replies
2.0k
views
News: supporting vg users on biostars
variation-graph genome vg vgteam
updated 11 months ago by 43k • written 4.7 years ago by ★ 2.4k
4
votes
4
replies
1.9k
views
News: 12th International Conference on Advancements in Bioinformatics and Drug Discovery
genome Computational-Biology
updated 12 months ago by 43k • written 6.0 years ago by ▴ 20
9
votes
4
replies
1.6k
views
News: Human Cell Atlas Data Coordination Platform Data Release Questionaire
RNA-Seq
updated 12 months ago by 43k • written 6.2 years ago by ★ 1.8k
10
votes
4
replies
1.8k
views
News: 3rd Berlin Summer School in NGS Data Analysis (2 seats just became available)
NGS RNA-Seq DNA-Seq
updated 11 months ago by 43k • written 5.3 years ago by 11k
6
votes
4
replies
1.3k
views
News: Course online - Comparative Genomics
assembly genome next-gen alignment
updated 11 months ago by 43k • written 4.1 years ago by ★ 2.5k
12
votes
4
replies
2.1k
views
News: #NGSchool2018 summer school in bioinformatics
NGSchool Personalised-Medicine Nanopore
updated 11 months ago by 43k • written 6.0 years ago by ▴ 290
2
votes
4
replies
1.2k
views
News: Course ONLINE - RNAseq data analysis with R and Bioconductor (15-19 June)
R RNA-seq Bioconductor
updated 11 months ago by 43k • written 4.0 years ago by ★ 2.5k
0
votes
4
replies
1.0k
views
News: Pan-Structural Variation hackathon in the Cloud!
SV sequencing
updated 11 months ago by 43k • written 4.3 years ago by 9.7k
9
votes
4
replies
2.5k
views
7 follow
News: fastp 0.22 released, with new FASTQ deduplication feature.
fastp
updated 9 months ago by 43k • written 2.7 years ago by ★ 2.5k
1
vote
3
replies
1.2k
views
News: 4th Berlin Summer School in NGS Data Analysis - October 5-9, 2020
NGS RNA-Seq DNA-Seq
updated 11 months ago by 43k • written 4.2 years ago by 11k
9
votes
3
replies
4.8k
views
News: Bioinformatics Contest 2020. Call for problems
contest
updated 11 months ago by 43k • written 4.7 years ago by ▴ 930
5
votes
3
replies
1.5k
views
News: Top GitHub repos for biomedicine
open-source software GitHub
updated 11 months ago by 43k • written 5.4 years ago by ▴ 50
4
votes
3
replies
1.1k
views
News: You may need to cleanup duplicate NCBI BLAST nt database volumes on your system
databases NCBI BLAST
8 months ago by PeterC_NCBI ▴ 410
2
votes
3
replies
1.7k
views
News: GCCBOSC 2018: A Bioinformatics Community Conference Call for Abstracts
Galaxy-Community-Conference BOSC GCC
updated 12 months ago by 43k • written 6.2 years ago by ★ 2.2k
0
votes
3
replies
1.4k
views
News: :: FINAL CALL :: A Practical Introduction to NGS Data Analysis (Nov 29 - Dec 1, 2023 in Munich, Germany) - only 2 seats left
DNA-Seq NGS RNA-Seq Workshop
6 months ago by David Langenberger 11k
0
votes
3
replies
1.0k
views
News: EMBO | EMBL Symposium: Seeing is Believing - Imaging the Molecular Processes of Life
image-analysis
updated 11 months ago by 43k • written 5.5 years ago by ▴ 10
2
votes
3
replies
1.4k
views
News: Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation
rna-extraction dna-extraction rna-seq
updated 11 months ago by 43k • written 5.7 years ago by ▴ 20
14
votes
3
replies
3.7k
views
News: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
seminar symposium conference
updated 11 months ago by 43k • written 6.0 years ago by 5.8k
4
votes
3
replies
3.2k
views
News: -max_target_seqs 1 in NCBI standalone BLAST does not do what you think it does
blast
updated 11 months ago by 43k • written 5.6 years ago by 11k
0
votes
2
replies
1.1k
views
News: Training - Introduction to Deep Learning
Deep-Learning Machine-Learning Python-Programming
updated 11 months ago by 43k • written 3.8 years ago by ★ 2.5k
1
vote
2
replies
1.7k
views
News: NCBI Datasets - try it out!
Assembly refseq genome ncbi
updated 11 months ago by 43k • written 4.1 years ago by ★ 3.7k
7
votes
2
replies
1.2k
views
News: NGS Data Analysis Workshops 2024
scRNA-seq dna-seq rna-seq nextflow
4 months ago by David Langenberger 11k
2
votes
2
replies
953
views
News: Interested in Machine Learning?
deep-learning machine-learning
updated 11 months ago by 43k • written 5.1 years ago by ★ 2.5k
4
votes
2
replies
1.3k
views
News: Hands-On Workshop: How to use bisulfite-treated sequencing to study DNA methylation (BS-Seq, Bisulfite-Seq, WGBS)
Workshop methylation bisulfite
updated 11 months ago by 43k • written 4.6 years ago by ★ 1.0k
3
votes
2
replies
1.0k
views
News: BETA Testing Opportunity for new RNA-seq data analysis tool
beta-testing RNA-seq multi-omics ngs
updated 11 months ago by 43k • written 5.3 years ago by • 0
1
vote
2
replies
277
views
News: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering Spatial-transcriptomics
updated 10 days ago by • 0 • written 11 days ago by ▴ 10
3
votes
2
replies
696
views
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
6 weeks ago by Johannes W. Dietrich • 0
0
votes
2
replies
706
views
News: Reduced functionality of Ensembl and Ensembl Genomes on the 13th November
ensembl
updated 11 months ago by 43k • written 4.5 years ago by 23k
1
vote
2
replies
770
views
News: Ensembl reduced functionality, early March
ensembl
updated 11 months ago by 43k • written 4.3 years ago by 23k
4
votes
2
replies
3.0k
views
News: New ebook: From cell line to Command line to learn computational biology
unix snakemake computational-biology RNA-seq
5 months ago by Ming Tommy Tang ★ 3.9k
6
votes
2
replies
1.1k
views
News: Temporarily reduced functionality of Ensembl and Ensembl Genomes
Ensembl
updated 11 months ago by 43k • written 5.3 years ago by ★ 2.4k
0
votes
2
replies
425
views
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
3 days ago by David Langenberger 11k
760 results • Page 1 of 16
Recent Votes
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
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 10
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 ▴ 10
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
Comment: How to generate table_annovar from VCF input? by Pierre Lindenbaum 161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem by Pierre Lindenbaum 161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences? by DGTool ▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by b.contreras.moreira ▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
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