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4
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Forum: [Meta] Use of AI
AI Artificial-Intelligence meta ChatGPT
updated 1 day ago by 39k • written 3 days ago by ★ 2.9k
2
votes
2
replies
181
views
Forum: Colleges
Colleges india universities
updated 6 days ago by 39k • written 7 days ago by • 0
19
votes
15
replies
1.3k
views
6 follow
Forum: Cross out line in Biostars
meta
updated 14 days ago by 39k • written 5.1 years ago by 5.3k
120
votes
33
replies
36k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 29 days ago by ★ 2.3k • written 9.8 years ago by 11k
100
votes
38
replies
28k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 29 days ago by 21k • written 9.6 years ago by ★ 3.6k
26
votes
12
replies
6.9k
views
6 follow
Forum: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
ngs
updated 4 weeks ago by ▴ 10 • written 9.6 years ago by ▴ 50
170
votes
43
replies
16k
views
25 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
updated 5 weeks ago by 11k • written 10.2 years ago by 98k
0
votes
2
replies
322
views
Forum: How to start in bioinformatics?
career
updated 27 days ago by 39k • written 7 weeks ago by • 0
3
votes
4
replies
595
views
Forum: I'm looking for a mentor in Bioinformatics
mentor teaching
7 weeks ago by cwaingartentrabajo • 0
12
votes
5
replies
748
views
6 follow
Forum: Bioinformatics opportunities in Europe?
career
updated 7 weeks ago by ▴ 20 • written 8 weeks ago by • 0
18
votes
14
replies
1.1k
views
7 follow
Forum: What's the general view on point & click bioinformatics for routine analyses?
ngs RNA-Seq next-gen-sequencing
6 weeks ago by Simon ▴ 40
0
votes
0
replies
3.6k
views
Forum: Optimal approach for variant calling with 3 diluted germline sample in one sequencing - Capture Sequencing
germline Calling Variant Capture Sequencing
8 weeks ago by Alexandre Eeckhoutte • 0
11
votes
11
replies
870
views
7 follow
Forum: Any tips in landing a bioinformatic job?
Spain R
updated 9 weeks ago by ★ 2.9k • written 9 weeks ago by ▴ 30
4
votes
2
replies
290
views
Forum: advice on course selection for a bioinformatics career.
career
updated 11 weeks ago by 98k • written 11 weeks ago by • 0
0
votes
1
reply
238
views
Forum: Graduate in molecular biology and genetics
biology genetics Molecular
updated 12 weeks ago by 129k • written 12 weeks ago by • 0
3
votes
1
reply
309
views
Forum: Open problems in genomics 2023
genomics pangenomics
updated 12 weeks ago by 129k • written 12 weeks ago by 4.9k
5
votes
3
replies
454
views
Forum: Someone posted the same question to StackOverflow and Biostars. The results will blow your mind.
meta
updated 3 months ago by 21k • written 3 months ago by ▴ 60
18
votes
10
replies
1.1k
views
Forum: Rust bioinformatics projects ideas
projects scRNA-seq RNA-seq Rust
3 months ago by bompipi95 ▴ 120
1
vote
0
replies
197
views
Forum: Penetrance versus heritability
penetrance heritability
3 months ago by tacrolimus ▴ 110
10
votes
15
replies
1.0k
views
Forum: How should reference genome fasta files be distributed by UCSC?
reference-genome fasta freeze ucsc-genome-browser
updated 5 days ago by 21k • written 3 months ago by ★ 1.5k
8
votes
4
replies
476
views
Forum: Implementing FAIR data principles to a bioinformatics lab
data
updated 3 months ago by 21k • written 3 months ago by ★ 1.5k
0
votes
0
replies
221
views
Forum: NGSrich - hg38
Coverage NGSrich
3 months ago by RK • 0
5
votes
5
replies
691
views
Forum: Bioinformatics - how to start?
molecular-biology
updated 3 months ago by ★ 23k • written 3 months ago by • 0
8
votes
8
replies
1.2k
views
7 follow
Forum: A Computer Scientist who wants to start Bioinformatics
computer-science books resources ngs
updated 4 months ago by ▴ 10 • written 5 months ago by • 0
7
votes
3
replies
658
views
Forum: Find a research paper for reproducing the results
research paper
updated 4 months ago by 129k • written 4 months ago by ★ 2.5k
1
vote
1
reply
417
views
Forum: Gene ontology vs Gene set enrichment
set enrichment GSEA ontology Gene analysis gene
updated 5 months ago by ★ 3.1k • written 5 months ago by • 0
6
votes
12
replies
1.1k
views
Forum: How to decide when to have local hardware vs cloud computing?
hardware computational-resources cloud
5 months ago by Lluís R. ★ 1.2k
15
votes
11
replies
1.9k
views
7 follow
Forum: BioStars and ChatGPT
ChatGPT Meta GPT
updated 7 weeks ago by ▴ 590 • written 6 months ago by ▴ 320
18
votes
10
replies
1.4k
views
7 follow
Forum: Add artificial intelligence training related disclaimers to your profile
licensing AI
updated 6 months ago by 52k • written 6 months ago by 98k
0
votes
2
replies
2.9k
views
Forum: Discussion question: Cutoff for SNP phylogeny
Phylogenetics SNP
6 months ago by SushiRoll ▴ 100
7
votes
2
replies
467
views
Forum: Improvement of Wikipedia articles with bioinformatic subjects
Wikipedia Bioinformatics
4 months ago by Matthias Zepper 3.7k
5
votes
4
replies
688
views
Forum: Best BAM viewer in 2022
bam sam tool-recommendation
6 months ago by Cornelius ▴ 60
1.2k
votes
206
replies
50k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 6 days ago by ★ 1.2k • written 12.2 years ago by 21k
8
votes
4
replies
737
views
Forum: GTF files from Ensembl Releases 105 and 106 unsorted
Ensembl bug GTF
6 months ago by dlaehnemann ▴ 10
10
votes
13
replies
1.8k
views
8 follow
Forum: Does a PhD or work experience set you up better to do bioinformatics work in industry?
advice industry phd
updated 6 months ago by 6.0k • written 6 months ago by ▴ 10
0
votes
2
replies
612
views
Forum: Best Phd Programs in Usa ( Computational Biology)
computational-biology drug-design
updated 6 months ago by 39k • written 8 months ago by • 0
4
votes
5
replies
699
views
6 follow
Forum: Which Bioinformatics Master's degree is better?
career masters
updated 18 days ago by 39k • written 7 months ago by • 0
1
vote
1
reply
513
views
Forum: Package is not available (for R version XXX)？ Manually download and install R packages
installation package R
updated 5 months ago by 4.9k • written 7 months ago by ▴ 30
3
votes
6
replies
652
views
Forum: How to become a moderator and other ways of contributing to Biostars
meta biostars
updated 18 days ago by 39k • written 8 months ago by 6.0k
2
votes
3
replies
567
views
Forum: Experiences with different cloud computing resources / providers
cloud pipeline rna-seq alignment
updated 8 months ago by 21k • written 8 months ago by ▴ 10
19
votes
13
replies
1.6k
views
8 follow
Forum: Can bioinformatics Phds be completely or almost completely done remotely?
PhD
updated 8 months ago by 6.1k • written 8 months ago by ▴ 40
8
votes
13
replies
1.6k
views
8 follow
Forum: Commercial software for genomics / NGS / bioinformatics
NGS software genomics
updated 9 months ago by • 0 • written 9 months ago by ★ 1.2k
4
votes
4
replies
912
views
Forum: Bioinformatics analogies
Bioinformatics
updated 9 months ago by 98k • written 9 months ago by ▴ 40
2
votes
4
replies
755
views
Forum: Is low N in-vivo research a blind spot for RNA-seq?
statistics metascience power sample-size
updated 10 weeks ago by 39k • written 9 months ago by ▴ 210
2
votes
4
replies
571
views
Forum: strand specific data
strand DNA RNA specific coding
9 months ago by upasana • 0
3
votes
0
replies
434
views
Forum: Let's build a list of Drug Databases including Tyrosine Kinase Inhibitors: Update 1
pharmacology RTK IC50 TKI database
9 months ago by Vincent Laufer ★ 2.9k
7
votes
14
replies
1.7k
views
7 follow
Forum: Why isn't GWAS used in oncology?
gwas association oncology studies somatic cancer
updated 9 months ago by 2.6k • written 10 months ago by ▴ 80
4
votes
4
replies
1.0k
views
Forum: Cloud Computing Services available?
resources Cloud-Computing
updated 6 months ago by 39k • written 11 months ago by ★ 2.3k
2
votes
7
replies
915
views
Forum: Build a Visual Analytic App for Rna-seq data [Ideas Accepted]
R plot rna-seq count
updated 10 months ago by 39k • written 10 months ago by ▴ 20
6
votes
3
replies
1.2k
views
Forum: Best formats for storing large amounts of data for random access
file-formats databases
updated 10 months ago by 3.7k • written 10 months ago by 17k
1,000 results • Page 1 of 20
Recent Votes
ChatGPT optimized for bioinformatics questions
ChatGPT optimized for bioinformatics questions
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
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Recent Replies
Comment: switching from illumination to NEB prep kits by GenoMax 129k
If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by Zhichao • 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values by ATpoint 72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2 by ATpoint 72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts by ATpoint 72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by ATpoint 72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values by ATpoint 72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments by Alexander ▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs by mhpakdel96 • 0
Thanks a lot, it works
Comment: Differential protein expression analysis by dsull ★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis by Ribo ▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values by Gordon Smyth ★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
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