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361
votes
57
replies
57k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 4 months ago by 84k • written 12.9 years ago by 96k
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
124
votes
46
replies
42k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq visualization deeptools ngsplot homer Forum
updated 18 months ago by ★ 2.3k • written 6.9 years ago by ★ 3.2k
292
votes
27
replies
41k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 6 months ago by 37k • written 7.0 years ago by ★ 2.4k
205
votes
58
replies
38k
views
31 follow
Forum: Will Python Take The Place Of R?
biopython statistics r python Forum
13 months ago by Medhat 9.5k
20
votes
12
replies
36k
views
7 follow
Forum: When To Use Sed Awk Over Perl Or Python
awk perl python Forum
updated 19 months ago by ▴ 140 • written 9.1 years ago by 9.5k
116
votes
31
replies
35k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 7 months ago by 37k • written 9.4 years ago by 11k
41
votes
17
replies
35k
views
15 follow
Forum: List Of Genome Sequencing Centers/Institutes
institutes bioinformatics genomics Forum
updated 16 months ago by 37k • written 9.9 years ago by 19k
113
votes
34
replies
35k
views
18 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow Forum
updated 3.5 years ago by ★ 9.2k • written 5.6 years ago by ▴ 760
11
votes
4
replies
33k
views
Forum: BWA command guide
BWA Page
updated 3 months ago by ▴ 10 • written 4.9 years ago by ★ 1.1k
21
votes
3
replies
31k
views
Forum: Did You Know That Researchgate Is Spamming Your Colleagues (Perhaps Without Your Explicit Consent)?
Forum
updated 10.0 years ago by 96k • written 10.0 years ago by 20k
46
votes
12
replies
31k
views
6 follow
Forum: BWA vs Bowtie 2 (Poll)
BWA Poll Bowtie2
updated 8 months ago by 37k • written 7.9 years ago by ▴ 270
251
votes
36
replies
30k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
file
updated 4 months ago by 84k • written 12.8 years ago by 152k
74
votes
14
replies
27k
views
12 follow
Forum: Bioinformatics Consulting Thoughts
consulting
updated 7 months ago by 37k • written 12.6 years ago by 4.5k
126
votes
44
replies
27k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
RNA-Seq NGS adapter Forum
written 6.4 years ago by ▴ 910
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
57
votes
19
replies
25k
views
6 follow
Forum: Attention: Bowtie2 And Multiple Hits
bowtie next-gen mapping Forum
updated 10.3 years ago by ▴ 150 • written 10.3 years ago by 9.8k
202
votes
41
replies
23k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 10 months ago by 37k • written 8.2 years ago by ★ 5.1k
151
votes
39
replies
22k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics Forum
updated 5.3 years ago by 84k • written 10.0 years ago by 3.0k
261
votes
47
replies
20k
views
35 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 25 days ago by 37k • written 7.7 years ago by ★ 4.2k
135
votes
41
replies
20k
views
20 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Forum
updated 9.3 years ago by ★ 1.1k • written 9.6 years ago by ★ 1.6k
106
votes
23
replies
20k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics Forum
written 9.0 years ago by ▴ 570
306
votes
65
replies
19k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 4 months ago by 84k • written 12.9 years ago by 27k
91
votes
20
replies
18k
views
15 follow
Forum: Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing
N-of-one WGS RNA-Seq next-gen Exome
updated 3 months ago by 37k • written 8.7 years ago by 20k
65
votes
26
replies
18k
views
13 follow
Forum: Macosx For Bioinformatics?
linux Forum
updated 9.2 years ago by 52k • written 9.2 years ago by 11k
284
votes
64
replies
17k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 4 months ago by 84k • written 11.9 years ago by 22k
279
votes
69
replies
17k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective Forum
updated 8 weeks ago by 37k • written 11.5 years ago by ▴ 160
84
votes
36
replies
16k
views
13 follow
Forum: Benchmark - Comparison of Different NGS Mappers
mRNA-Seq benchmark NGS-mapper
updated 10 months ago by 37k • written 8.1 years ago by 9.8k
160
votes
22
replies
16k
views
19 follow
Forum: Advice For Newcomers To The Bioinformatics Field
advice career
updated 11 weeks ago by 37k • written 9.6 years ago by 9.5k
36
votes
21
replies
16k
views
9 follow
Forum: What Is Your Favorite Conserved Protein?
protein conservation Forum
updated 9.4 years ago by ★ 1.1k • written 9.4 years ago by 11k
33
votes
5
replies
15k
views
9 follow
Forum: How do I explain to my non-bioinformatician labmates how to interpret principal components?
RNA-Seq communication analysis pca
updated 5 months ago by 37k • written 7.1 years ago by ▴ 610
31
votes
13
replies
15k
views
8 follow
Forum: Should I Pursue A Bioinformatics Msc?
bioinformatics Forum
updated 10.0 years ago by ★ 4.0k • written 10.0 years ago by ▴ 70
48
votes
38
replies
15k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
genome annotation software Forum
updated 6.9 years ago by ▴ 360 • written 6.9 years ago by 11k
159
votes
38
replies
14k
views
22 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
bioinformatics Forum humor
updated 4 months ago by ▴ 30 • written 9.8 years ago by 96k
9
votes
9
replies
14k
views
6 follow
Forum: Open Source Bioinformatics projects for beginners
Begginers Bioinformatics Open Source Forum
updated 5.0 years ago by ★ 2.4k • written 5.0 years ago by ▴ 40
93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
Forum
updated 9.2 years ago by ▴ 370 • written 9.2 years ago by 96k
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 8 weeks ago by 37k • written 9.7 years ago by 9.5k
64
votes
29
replies
14k
views
15 follow
Forum: Fundamentals Of Designing Biological Databases?
database tutorial Forum
updated 5.0 years ago by ▴ 180 • written 12.2 years ago by ▴ 130
61
votes
11
replies
14k
views
9 follow
Forum: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
programming Forum
updated 10 months ago by 37k • written 9.6 years ago by 19k
42
votes
21
replies
14k
views
10 follow
Forum: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
1000genomes selection human Forum
updated 9 months ago by 37k • written 8.9 years ago by 27k
19
votes
0
replies
13k
views
Forum: Hadley Wickham of ggplot and RStudio uses this
uses-this Forum
updated 22 months ago by 37k • written 8.3 years ago by 96k
57
votes
43
replies
13k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
RNA-Seq NGS alignment genome sequence Forum
updated 23 months ago by ▴ 50 • written 4.0 years ago by 9.8k
0
votes
0
replies
13k
views
Forum: Characteristics Analysis of Biotechnology Industry
biotechnology-industry
updated 6 months ago by 37k • written 7.8 years ago by • 0
20
votes
22
replies
12k
views
11 follow
Forum: Nextseq for analysts
nextseq basespace casava bcl2fastq Forum
updated 4 months ago by 37k • written 8.6 years ago by 5.3k
8
votes
2
replies
12k
views
Forum: List of popular bioinformatics software/tools
bioinformatic sofwares Forum
updated 12 months ago by 37k • written 8.3 years ago by ▴ 20
47
votes
19
replies
11k
views
10 follow
Forum: Is Software Development a key part of Bioinformatics?
Software-Development
updated 5 months ago by 37k • written 8.1 years ago by ▴ 70
105
votes
46
replies
11k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Forum
written 9.4 years ago by ★ 1.1k
6
votes
12
replies
11k
views
11 follow
Forum: Online/remote/distance learning/ - partime/fulltime - PhD, Bioinformatics in USA
PhD university Forum
updated 21 months ago by 37k • written 6.3 years ago by ▴ 20
61
votes
70
replies
11k
views
21 follow
Forum: Biostar 2.0 released
biostar Forum
updated 16 months ago by 37k • written 8.8 years ago by 96k
60
votes
14
replies
10k
views
14 follow
Forum: Interesting bioinformatics blogs (2017 edition)
blogs Forum
updated 4.6 years ago by ▴ 710 • written 5.8 years ago by 47k
1,000 results • Page 1 of 20
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
Popular Question to tianshenbio ▴ 160
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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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