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359 results • Page 1 of 8
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7
votes
3
replies
406
views
Forum: Find a research paper for reproducing the results
research paper
updated 15 days ago by 125k • written 16 days ago by ★ 2.5k
7
votes
7
replies
721
views
6 follow
Forum: A Computer Scientist who wants to start Bioinformatics
computer-science books resources ngs
updated 5 weeks ago by ★ 3.7k • written 5 weeks ago by • 0
0
votes
1
reply
245
views
Forum: Gene ontology vs Gene set enrichment
set enrichment GSEA ontology Gene analysis gene
updated 6 weeks ago by ★ 1.7k • written 6 weeks ago by • 0
6
votes
12
replies
686
views
Forum: How to decide when to have local hardware vs cloud computing?
hardware computational-resources cloud
7 weeks ago by Lluís R. ★ 1.2k
15
votes
10
replies
1.2k
views
6 follow
Forum: BioStars and ChatGPT
ChatGPT Meta GPT
updated 7 weeks ago by 1.8k • written 7 weeks ago by ▴ 280
18
votes
10
replies
912
views
7 follow
Forum: Add artificial intelligence training related disclaimers to your profile
licensing AI
updated 7 weeks ago by 52k • written 7 weeks ago by 96k
0
votes
2
replies
1.2k
views
Forum: Discussion question: Cutoff for SNP phylogeny
Phylogenetics SNP
8 weeks ago by SushiRoll ▴ 100
7
votes
2
replies
275
views
Forum: Improvement of Wikipedia articles with bioinformatic subjects
Wikipedia Bioinformatics
4 days ago by Matthias Zepper 2.8k
5
votes
4
replies
440
views
Forum: Best BAM viewer in 2022
bam sam tool-recommendation
8 weeks ago by Cornelius ▴ 30
1.2k
votes
205
replies
47k
views
107 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 11 days ago by ▴ 240 • written 11.8 years ago by 21k
8
votes
4
replies
386
views
Forum: GTF files from Ensembl Releases 105 and 106 unsorted
Ensembl bug GTF
9 weeks ago by dlaehnemann ▴ 10
10
votes
13
replies
1.1k
views
8 follow
Forum: Does a PhD or work experience set you up better to do bioinformatics work in industry?
advice industry phd
updated 11 weeks ago by 5.7k • written 11 weeks ago by ▴ 10
0
votes
2
replies
457
views
Forum: Best Phd Programs in Usa ( Computational Biology)
computational-biology drug-design
updated 7 weeks ago by 37k • written 3 months ago by • 0
4
votes
5
replies
505
views
6 follow
Forum: Which Bioinformatics Master's degree is better?
bioifnormatics masters
updated 12 weeks ago by ▴ 100 • written 12 weeks ago by • 0
1
vote
1
reply
375
views
Forum: Package is not available (for R version XXX)？ Manually download and install R packages
installation package R
updated 26 days ago by 4.4k • written 3 months ago by ▴ 30
99
votes
36
replies
26k
views
32 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 5 days ago by 21k • written 9.2 years ago by ★ 3.6k
3
votes
6
replies
462
views
Forum: How to become a moderator and other ways of contributing to Biostars
biostars
3 months ago by iraun 5.7k
2
votes
3
replies
388
views
Forum: Experiences with different cloud computing resources / providers
cloud pipeline rna-seq alignment
updated 4 months ago by 21k • written 4 months ago by ▴ 10
19
votes
13
replies
1.1k
views
8 follow
Forum: Can bioinformatics Phds be completely or almost completely done remotely?
PhD
updated 4 months ago by 5.8k • written 4 months ago by ▴ 40
8
votes
13
replies
1.2k
views
8 follow
Forum: Commercial software for genomics / NGS / bioinformatics
NGS software genomics
updated 4 months ago by • 0 • written 4 months ago by ★ 1.1k
4
votes
4
replies
686
views
Forum: Bioinformatics analogies
Bioinformatics
updated 4 months ago by 96k • written 4 months ago by ▴ 40
2
votes
4
replies
591
views
Forum: Is low N in-vivo research a blind spot for RNA-seq?
power metascience statistics sample size
updated 5 months ago by 16k • written 5 months ago by ▴ 210
2
votes
4
replies
424
views
Forum: strand specific data
strand DNA RNA specific coding
5 months ago by upasana • 0
3
votes
0
replies
294
views
Forum: Let's build a list of Drug Databases including Tyrosine Kinase Inhibitors: Update 1
pharmacology RTK IC50 TKI database
5 months ago by Vincent Laufer ★ 2.5k
7
votes
14
replies
1.4k
views
7 follow
Forum: Why isn't GWAS used in oncology?
gwas association oncology studies somatic cancer
updated 5 months ago by 1.8k • written 5 months ago by ▴ 80
4
votes
4
replies
804
views
Forum: Cloud Computing Services available?
resources Cloud-Computing
updated 7 weeks ago by 37k • written 7 months ago by ★ 2.2k
2
votes
7
replies
738
views
Forum: Build a Visual Analytic App for Rna-seq data [Ideas Accepted]
R plot rna-seq count
updated 6 months ago by 37k • written 6 months ago by ▴ 20
6
votes
3
replies
703
views
Forum: Best formats for storing large amounts of data for random access
file-formats databases
updated 6 months ago by 2.8k • written 6 months ago by 16k
0
votes
1
reply
281
views
Forum: Add an intercept column to a bed file
plink intercept bed
updated 6 months ago by 68k • written 6 months ago by • 0
4
votes
2
replies
1.3k
views
Forum: Best resource for getting a person with a Math/Comp Sci background the right amount of Biology knowledge
biology teaching
updated 6 weeks ago by 37k • written 6 months ago by ★ 2.5k
0
votes
0
replies
290
views
Forum: Normalization of ChIP-seq _ Spikein normalization + RPGC
ChIP-seq normalization RPGC Spikein Normalization
6 months ago by goddy93 • 0
3
votes
1
reply
339
views
Forum: Would an automated NGS analytics platform help research?
ngs data-analysis
updated 6 months ago by 37k • written 6 months ago by • 0
5
votes
2
replies
479
views
Forum: Skills for industry career in bioinformatics
industry
updated 6 months ago by 10k • written 6 months ago by ▴ 10
9
votes
6
replies
680
views
Forum: Programming languages in industry
programming language
updated 6 months ago by 9.5k • written 6 months ago by ▴ 30
2
votes
6
replies
667
views
Forum: Getting the best of RNA-Seq
RNA-Seq isoform gene expression
7 months ago by Antonio R. Franco ★ 5.0k
1
vote
0
replies
298
views
Forum: Not all Over Representation Analyses are the same!
clusterProfiler Analysis fisher hypergeometric ORA Pathway
7 months ago by Francesco ▴ 20
3
votes
2
replies
472
views
Forum: From protein-protein interaction networks to..
limitations tools knowledge computational workflow
7 months ago by BioInfoBeginner ▴ 40
0
votes
0
replies
351
views
Forum: Best practices for merging vcfs with different positions + different samples?
vcf bcftools genotypes
updated 6 weeks ago by 37k • written 7 months ago by ▴ 30
24
votes
6
replies
4.0k
views
6 follow
Forum: Awk in Bioinformatics
perl awk shell
updated 8 weeks ago by 37k • written 4.4 years ago by ★ 9.2k
7
votes
8
replies
949
views
Forum: Can we lock posts related to merging vcf files?
vcf
updated 8 weeks ago by 37k • written 8 months ago by 2.6k
0
votes
0
replies
327
views
Forum: Bioinformatics for understanding cancer and other diseases
cancer omics
updated 6 weeks ago by 37k • written 8 months ago by ★ 1.4k
1
vote
3
replies
894
views
Forum: What counts as a valid biological replicate in single cell RNAseq?
statistics biological replicates scRNA-seq
updated 8 months ago by 3.4k • written 8 months ago by • 0
3
votes
3
replies
490
views
Forum: Looking for a PostDoc position in ML-heavy medical bioinformatics in Germany
Germany PostDoc
updated 8 months ago by 26k • written 8 months ago by ★ 2.9k
0
votes
0
replies
90
views
Forum: Can Bioinformatics be used in developing a product?
product company business
updated 6 weeks ago by 37k • written 8 months ago by ▴ 10
0
votes
2
replies
575
views
Forum: Bioinformatics algorithm tutorials in C++/C
protein gene genome
updated 8 months ago by 52k • written 8 months ago by ▴ 970
34
votes
11
replies
7.7k
views
13 follow
Forum: Gallery: Computational tools for DNA methylation
computational-tools methylation
updated 5 months ago by 37k • written 7.2 years ago by ★ 9.2k
6
votes
8
replies
1.1k
views
Forum: PC build for Nanopore data analysis
python PC pipeline nanopore-sequencing
8 months ago by stan.aanhane ▴ 30
7
votes
6
replies
794
views
Forum: How to learn bioinformatics?
learning
updated 6 weeks ago by 37k • written 8 months ago by ▴ 10
2
votes
3
replies
412
views
Forum: What is difference between Bioinformatics and Data Science?
Data-Science
updated 6 weeks ago by 37k • written 8 months ago by ▴ 30
2
votes
2
replies
557
views
Forum: Project ideas
project-ideas
updated 8 months ago by 52k • written 8 months ago by • 0
359 results • Page 1 of 8
Recent Votes
A: Using ColSums vs sizeFactors in read count normalization
Comment: a problem with getBM
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
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Teacher to ATpoint 68k
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Recent Replies
Answer: how to do a reliable single cell sequencing analysis? by ATpoint 68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM by sanaz • 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v by fuellen ▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM by Mike Smith ★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome by congliu37 • 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File? by Jeremy Leipzig 21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)? by Fabio Marroni ★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism by Rob ▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers by Pierre Lindenbaum 152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence by vvasta • 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation? by Fabio Marroni ★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2 by Fabio Marroni ★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file** by Pierre Lindenbaum 152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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