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1,000 results • Page 1 of 20
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1.2k
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206
replies
50k
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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
361
votes
57
replies
61k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 8 months ago by 85k • written 13.3 years ago by 98k
306
votes
65
replies
20k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 8 months ago by 85k • written 13.3 years ago by 27k
294
votes
27
replies
42k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 10 months ago by 39k • written 7.4 years ago by ★ 2.4k
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 4 months ago by 39k • written 10.1 years ago by 9.6k
286
votes
64
replies
18k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 8 months ago by 85k • written 12.2 years ago by 22k
279
votes
69
replies
18k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective
updated 3 months ago by 39k • written 11.9 years ago by ▴ 160
262
votes
48
replies
21k
views
37 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 3 months ago by ▴ 970 • written 8.1 years ago by ★ 4.2k
251
votes
36
replies
31k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
project-management file-management
updated 10 weeks ago by 39k • written 13.1 years ago by 154k
244
votes
36
replies
8.1k
views
32 follow
Forum: Good Habit for Bioinformatics Analyst or Scientist
Analyst Scientist
updated 8 weeks ago by 39k • written 7.1 years ago by ★ 9.3k
206
votes
58
replies
39k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 3 months ago by 39k • written 10.1 years ago by 9.6k
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 3 months ago by 39k • written 8.6 years ago by ★ 5.2k
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
160
votes
22
replies
16k
views
19 follow
Forum: Advice For Newcomers To The Bioinformatics Field
advice career
updated 7 months ago by 39k • written 9.9 years ago by 9.6k
151
votes
39
replies
23k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 3 months ago by 39k • written 10.4 years ago by 3.0k
145
votes
56
replies
7.5k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 3 months ago by 39k • written 10.2 years ago by 98k
144
votes
62
replies
9.6k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 3 months ago by 39k • written 12.3 years ago by ★ 2.9k
138
votes
42
replies
20k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 10 weeks ago by ★ 2.9k • written 10.0 years ago by ★ 1.6k
134
votes
65
replies
3.9k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate
updated 20 hours ago by 39k • written 3.5 years ago by ▴ 880
129
votes
38
replies
6.0k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 7 days ago by 39k • written 4.2 years ago by 98k
126
votes
44
replies
28k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 12 weeks ago by 39k • written 6.7 years ago by ▴ 970
125
votes
46
replies
44k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 8 weeks ago by 39k • written 7.3 years ago by ★ 3.2k
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
116
votes
35
replies
7.2k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 3 months ago by 39k • written 10.2 years ago by 21k
115
votes
35
replies
38k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 25 days ago by 39k • written 6.0 years ago by ▴ 760
113
votes
53
replies
5.3k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 7 days ago by 39k • written 4.2 years ago by ▴ 170
106
votes
23
replies
20k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 3 months ago by 39k • written 9.3 years ago by ▴ 590
105
votes
46
replies
12k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 3 months ago by 39k • written 9.8 years ago by ★ 1.1k
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
99
votes
21
replies
8.0k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 3 months ago by 39k • written 10.4 years ago by ▴ 370
98
votes
41
replies
4.6k
views
17 follow
Forum: I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error next-gen-sequencing
updated 8 weeks ago by 39k • written 6.8 years ago by ▴ 500
93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 3 months ago by 39k • written 9.5 years ago by 98k
91
votes
20
replies
19k
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 7 months ago by 39k • written 9.1 years ago by 20k
88
votes
24
replies
4.9k
views
10 follow
Forum: How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 3 months ago by 39k • written 10.3 years ago by 1.9k
86
votes
29
replies
8.7k
views
9 follow
Forum: What is the future of EMBL-EBI (and European bioinformatics in general) in case of a 'Brexit'?
EU brexit EBI politics
updated 8 weeks ago by 39k • written 7.0 years ago by 52k
84
votes
22
replies
3.7k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 12 weeks ago by 39k • written 4.0 years ago by ▴ 180
83
votes
30
replies
5.7k
views
18 follow
Forum: Optimal design for bioinformatics "lab" space?
design lab-space
updated 11 months ago by 39k • written 8.2 years ago by 18k
82
votes
32
replies
6.6k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 3 months ago by 39k • written 10.5 years ago by ★ 3.6k
81
votes
21
replies
4.2k
views
16 follow
Forum: [UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 11 weeks ago by 39k • written 7.0 years ago by ★ 3.2k
80
votes
34
replies
4.1k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 5 months ago by 39k • written 8.0 years ago by ▴ 520
80
votes
23
replies
4.5k
views
11 follow
Forum: Are we facing a bioinformatician shortage?
salary career
updated 12 weeks ago by 39k • written 8.6 years ago by ★ 3.0k
79
votes
35
replies
8.1k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 9 days ago by • 0 • written 7.6 years ago by ▴ 650
78
votes
31
replies
5.8k
views
14 follow
Forum: Do Bad Questions Even Exist?
biostars general education
updated 3 months ago by 39k • written 12.3 years ago by 10k
74
votes
14
replies
28k
views
12 follow
Forum: Bioinformatics Consulting Thoughts
consulting
updated 11 months ago by 39k • written 13.0 years ago by 4.5k
72
votes
18
replies
6.8k
views
17 follow
Forum: What Is One Book Every Bioinformatician Should Read?
books
updated 3 months ago by 39k • written 9.9 years ago by 7.8k
72
votes
28
replies
5.4k
views
10 follow
Forum: Bioinformatics commercial services as a risk factor for scientific misconduct
commercial-services ethics misconduct
updated 11 months ago by 39k • written 8.4 years ago by ▴ 90
70
votes
19
replies
4.7k
views
13 follow
Forum: Thrown Into A Bioinformatics Position
computational-analysis
updated 10 months ago by 39k • written 7.7 years ago by ▴ 170
69
votes
39
replies
3.4k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 25 days ago by 39k • written 6.0 years ago by 13k
68
votes
48
replies
7.1k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2
updated 25 days ago by 39k • written 5.9 years ago by 98k
68
votes
22
replies
6.6k
views
16 follow
Forum: Learning Python: list of resources
python
updated 8 weeks ago by 39k • written 6.6 years ago by ★ 2.8k
1,000 results • Page 1 of 20
Recent Votes
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
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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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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