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1.2k
votes
205
replies
48k
views
107 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 9 weeks ago by ▴ 250 • written 12.0 years ago by 21k
730
votes
161
replies
108k
views
100 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 10 days ago by 1.6k • written 6.3 years ago by 97k
361
votes
57
replies
59k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 6 months ago by 84k • written 13.1 years ago by 97k
358
votes
79
replies
136k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 4 months ago by 38k • written 10.1 years ago by ★ 4.3k
328
votes
54
replies
57k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 6 months ago by 84k • written 13.0 years ago by 24k
319
votes
90
replies
214k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 6 months ago by 38k • written 12.2 years ago by 4.8k
306
votes
65
replies
19k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 6 months ago by 84k • written 13.1 years ago by 27k
298
votes
121
replies
25k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 7 weeks ago by ▴ 250 • written 12.7 years ago by 11k
294
votes
27
replies
41k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 7 months ago by 38k • written 7.2 years ago by ★ 2.4k
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 6 weeks ago by 38k • written 9.9 years ago by 9.6k
286
votes
64
replies
18k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 6 months ago by 84k • written 12.0 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 5 weeks ago by 38k • written 11.6 years ago by ▴ 160
276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 15 hours ago by 38k • written 8.6 years ago by 20k
274
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 24 days ago by 38k • written 9.4 years ago by 20k
267
votes
29
replies
251k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 4 months ago by 38k • written 10.4 years ago by ▴ 610
262
votes
48
replies
20k
views
37 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 26 days ago by ▴ 970 • written 7.9 years ago by ★ 4.2k
251
votes
36
replies
30k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
project-management file-management
updated 1 day ago by 38k • written 12.9 years ago by 153k
244
votes
36
replies
7.8k
views
32 follow
Forum: Good Habit for Bioinformatics Analyst or Scientist
Habit Analyst Scientist Forum
6.1 years ago by Shicheng Guo ★ 9.3k
238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.6 years ago by ★ 4.6k
235
votes
45
replies
69k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen sequencing illumina exome human
updated 11.8 years ago by ▴ 50 • written 12.8 years ago by 4.8k
226
votes
39
replies
281k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 7 months ago by 38k • written 13.4 years ago by ▴ 620
223
votes
38
replies
134k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 3 months ago by ▴ 90 • written 10.1 years ago by 19k
206
votes
58
replies
38k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 28 days ago by 38k • written 9.8 years ago by 9.5k
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 6 weeks ago by 38k • written 8.4 years ago by ★ 5.2k
197
votes
27
replies
30k
views
20 follow
Bioinformatics Cartoon
bioinformatics
updated 5 weeks ago by 38k • written 11.2 years ago by ★ 2.3k
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 weeks ago by 38k • written 10.5 years ago by 20k
188
votes
21
replies
163k
views
11 follow
Forward And Reverse Strand Conventions
sequence strand
updated 4 months ago by 97k • written 12.4 years ago by ★ 2.8k
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 5 months ago by 38k • written 12.4 years ago by ▴ 340
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 6 months ago by 38k • written 13.0 years ago by ★ 1.6k
184
votes
45
replies
29k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
general pipeline
updated 18 months ago by 38k • written 13.1 years ago by 27k
179
votes
51
replies
15k
views
26 follow
I Am Preparing A Course On Ngs: Any Suggestion ?
next-gen sequencing galaxy
updated 9.7 years ago by ▴ 600 • written 12.4 years ago by 153k
173
votes
30
replies
88k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 14 months ago by 38k • written 11.9 years ago by ▴ 610
172
votes
34
replies
23k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r bioconductor books
updated 8.4 years ago by ★ 1.6k • written 13.0 years ago by 52k
171
votes
26
replies
6.8k
views
12 follow
How Do You Acknowledge Biostar And Its Contributors In Your Research Output?
meta biostars
updated 5 weeks ago by 38k • written 12.1 years ago by 3.2k
167
votes
41
replies
85k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence fasta
updated 7 weeks ago by • 0 • written 11.8 years ago by ▴ 240
164
votes
70
replies
55k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 11.2 years ago by ▴ 430 • written 11.7 years ago by ★ 1.8k
160
votes
22
replies
16k
views
19 follow
Forum: Advice For Newcomers To The Bioinformatics Field
advice career
updated 4 months ago by 38k • written 9.7 years ago by 9.5k
160
votes
52
replies
116k
views
28 follow
Fastq Convert To Fasta
perl
9.4 years ago by biolab ★ 1.4k
159
votes
38
replies
15k
views
22 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
updated 29 days ago by 38k • written 10.0 years ago by 97k
158
votes
8
replies
151k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix
updated 8 months ago by 38k • written 10.3 years ago by ▴ 430
158
votes
19
replies
36k
views
16 follow
Why Does Rna-Seq Read Count Fit Poisson Distribution?
rna-seq modeling
updated 15 months ago by 38k • written 9.4 years ago by ▴ 730
157
votes
62
replies
74k
views
37 follow
Selecting Random Pairs From Fastq?
random fastq sequence illumina code
updated 9 months ago by • 0 • written 12.0 years ago by 4.1k
154
votes
17
replies
27k
views
13 follow
What Are The Big Questions That Bioinformatics And Computational Biology Will Be Answering In The Next Few Years?
updated 8 months ago by 38k • written 11.2 years ago by 26k
153
votes
27
replies
9.3k
views
21 follow
The Best Question To Ask In A Bioinformatics Seminar
subjective
updated 12.2 years ago by ★ 1.1k • written 12.3 years ago by 27k
153
votes
32
replies
7.0k
views
23 follow
Picking A Programming Language And Where To Begin
programming next-gen sequencing c subjective
updated 11.1 years ago by ▴ 60 • written 11.6 years ago by ★ 2.8k
152
votes
24
replies
59k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
splicing tools rna-seq alternative-splicing
updated 8 months ago by 38k • written 10.1 years ago by 10k
152
votes
44
replies
28k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 8 months ago by 38k • written 9.2 years ago by ★ 2.0k
151
votes
39
replies
22k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 29 days ago by 38k • written 10.2 years ago by 3.0k
151
votes
42
replies
174k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 10 months ago by 38k • written 11.1 years ago by 20k
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 29 days ago by 38k • written 10.3 years ago by ★ 1.6k
1,000 results • Page 1 of 20
Recent Votes
Difference between RNA-sq and Transcriptome
Rat lung transcriptome
A: microarray, RNAseq, CEL, edgeR, etc. for DGE analysis
Converting SNP from chr:pos to rs number using PLINK?
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
Answer: Cellranger sequencing
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
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Recent Replies
Comment: Remove part of headers in FASTA file by Pierre Lindenbaum 153k
Use `cut -d ' '`
Answer: Problem running interproscan-5.15-54.0 for protein sequences by Pratyay • 0
Hi, can you guide me how to compile the src folder? Many thanks!
Comment: Matching gene-expression data with clinical data: best practices. by krushnach80 ★ 1.1k
You can check [this][1] [1]: https://www.linkedomics.org/
Answer: Matching gene-expression data with clinical data: best practices. by jose.sgomez94 • 0
Figured out one can use the TCGAutils package in R and UUIDtobarcode() function. Still, suggestions of best practices would be awesome!
Answer: Understanding multifactor designs and control variables in DESeq2 by FrankStarling ▴ 50
https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2021/RNAseq/Markdowns/10_DE_analysis_with_DESeq2.Solutions.html …
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by Adaline.D • 0
I appreciate your help, LChart! I will use raw data in case of a substantial loss of power. (1) The publication did a PCA and then analy…
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by LChart 2.2k
Short answer: use LIMMA Long answer: edgeR uses a negative binomial model, and expects *counts* and not *values*. Please read section 2.8.…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Wayne, both of these methods work beautifully. I really appreciate the detail you provided, thank you so much for your help!
Comment: Ortholog assembly and extraction by dthorbur ▴ 420
I really like `orthofinder` and use it frequently, but there are also plenty of other tools out there. [Here](https://academic.oup.com/mbe/…
Comment: chloroplast genome gaps by ugur • 0
after alignment, it occurs in different sizes of gaps
Answer: Cellranger sequencing by ATpoint 70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
Answer: Assembly at lineage level from shotgun data ? by Mensur Dlakic ★ 23k
The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a referenc…
Comment: Ortholog assembly and extraction by GenoMax 127k
Many seem to use `orthofinder` for this purpose. See if it is useful: https://github.com/davidemms/OrthoFinder
Answer: Python formatting when visualizing Primer3-py dimers by Wayne ★ 1.7k
Try this so you'll see that using [tabulate](https://github.com/astanin/python-tabulate) to print the dataframe causes it to respect the li…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Glad I am making this more clear. The 'test1' in practice will be the 'primer name' to allow for tracking of other metrics (Tm, hairpin str…
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