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50
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4.4k
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Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 6 months ago by 40k • written 4.7 years ago by 76k
49
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
48
votes
28
replies
8.5k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
4 months ago by Ram 40k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 8 months ago by 40k • written 10.6 years ago by 98k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 7 months ago by 40k • written 11.5 years ago by ▴ 540
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 5 months ago by 40k • written 7.5 years ago by ★ 3.2k
43
votes
6
replies
21k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 20 months ago by ▴ 40 • written 2.5 years ago by 12k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 6 months ago by 40k • written 9.7 years ago by 6.0k
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
42
votes
16
replies
22k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 13 months ago by 40k • written 8.0 years ago by ★ 2.4k
42
votes
19
replies
7.4k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 7 months ago by 40k • written 10.6 years ago by 4.1k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 6 months ago by 40k • written 9.5 years ago by ★ 1.9k
39
votes
6
replies
18k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 4 months ago by 40k • written 6.1 years ago by ★ 3.3k
39
votes
8
replies
11k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
36
votes
5
replies
5.8k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 17 days ago by ▴ 20 • written 8.2 years ago by ▴ 410
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 4 months ago by 134k • written 9.8 years ago by 20k
34
votes
15
replies
5.8k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 6 months ago by 40k • written 4.3 years ago by ★ 9.3k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 6 months ago by 40k • written 7.0 years ago by ▴ 310
33
votes
9
replies
30k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 6 months ago by 40k • written 3.1 years ago by ▴ 160
32
votes
4
replies
7.0k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 6 months ago by 40k • written 4.9 years ago by ★ 1.6k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 6 months ago by 40k • written 3.3 years ago by 86k
31
votes
12
replies
28k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 6 months ago by 40k • written 9.9 years ago by 98k
31
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 6 months ago by 40k • written 9.5 years ago by ▴ 810
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 12 months ago by 40k • written 11.4 years ago by 98k
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 7 months ago by 40k • written 10.6 years ago by 6.0k
29
votes
5
replies
6.1k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 6 months ago by 40k • written 10.0 years ago by ★ 4.3k
28
votes
4
replies
4.0k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 6 months ago by 40k • written 4.7 years ago by 26k
28
votes
13
replies
11k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 20 months ago by ★ 1.2k • written 23 months ago by 98k
27
votes
0
replies
3.2k
views
Tutorial: Building Docker images
singularity docker container
14 months ago by ATpoint 76k
27
votes
10
replies
69k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 6 months ago by 40k • written 2.5 years ago by ★ 1.4k
26
votes
17
replies
7.1k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 12 months ago by 40k • written 9.1 years ago by 6.0k
26
votes
0
replies
2.3k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 6 months ago by 40k • written 3.9 years ago by 19k
25
votes
15
replies
8.4k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 7 months ago by 40k • written 10.7 years ago by 9.7k
24
votes
4
replies
6.9k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 6 months ago by 40k • written 4.1 years ago by 76k
23
votes
8
replies
5.1k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 21 months ago by 40k • written 9.1 years ago by 24k
23
votes
19
replies
6.1k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 5 months ago by 40k • written 7.0 years ago by ★ 2.4k
22
votes
1
reply
3.1k
views
Tutorial: Introduction To R Course Materials Available
R
updated 8 months ago by 40k • written 11.4 years ago by 26k
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 5 months ago by 40k • written 6.9 years ago by ★ 2.1k
21
votes
2
replies
4.8k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 12 months ago by ▴ 40 • written 2.4 years ago by 8.2k
21
votes
9
replies
6.3k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 7 months ago by 40k • written 10.3 years ago by 9.7k
21
votes
10
replies
6.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 6 months ago by 40k • written 3.1 years ago by 12k
20
votes
7
replies
6.0k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 6 months ago by 40k • written 5.0 years ago by ▴ 760
20
votes
4
replies
2.4k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 6 months ago by 40k • written 4.4 years ago by ▴ 180
20
votes
6
replies
5.2k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 6 months ago by 40k • written 7.0 years ago by ★ 5.2k
20
votes
2
replies
7.6k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 4 months ago by 40k • written 5.8 years ago by ★ 3.4k
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 5 months ago by 40k • written 7.0 years ago by ★ 4.2k
20
votes
0
replies
8.5k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
20
votes
14
replies
3.6k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 5 months ago by 40k • written 7.4 years ago by ▴ 460
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 7 months ago by 40k • written 10.5 years ago by 20k
20
votes
5
replies
6.5k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 5 months ago by 40k • written 7.2 years ago by ★ 1.5k
379 results • Page 2 of 8
Recent Votes
Human Genomics Team Leader
Comment: Low Alignment rate
Answer: Filter transcription factors
Answer: Filter transcription factors
Answer: Filter transcription factors
Comment: Integrated Seurat object change name of the two conditions
Comment: Integrated Seurat object change name of the two conditions
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Popular Question to adeizadavid ▴ 10
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Recent Replies
Answer: How to find the most representative protein data base ID for your protein? by GenoMax 134k
Option 1: Use MANE select proteins that you can download here (latest release as of today will keep changing) : https://ftp.ncbi.nlm.nih.g…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by ATpoint 76k
Never tried, so idk. Why wouldn't it support it?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by ATpoint 76k
I never tried conda images but since `mamba > conda` I guess mambaforge is better.
Comment: Filter human transcription factors by Chris ▴ 180
Thank you so much!
Comment: Filter human transcription factors by Chris ▴ 180
Yes, I do GO and GSEA to get pathway. I download the background gene at https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C3 Th…
Answer: Visualize where kmers are on a reference genome by Alex Reynolds 35k
Make a bigBed file: https://www.biostars.org/p/9546293/ Then view it on the UCSC Genome Browser: http://genome.ucsc.edu/goldenPath/help/…
Comment: Integrated Seurat object change name of the two conditions by camillab. ▴ 130
great! thank you very much!
Answer: Filter transcription factors by jared.andrews07 ★ 15k
[This database](http://humantfs.ccbr.utoronto.ca/download.php) has been the best I've found.
Comment: Filter transcription factors by Ram 40k
What have you tried? Have you looked at GO annotations?
Comment: how to identify uniq genes between two gff files. by nikhil ▴ 10
yes @juke34 , I tried agat_sp_compare_two_annotations.pl for both gff files and got comparative output in table format. Thank you very muc…
Comment: Integrated Seurat object change name of the two conditions by Amitm ★ 2.2k
Yes, its similar structure. This snippet should add a new metadata column "sample.New" with what you want to do # Assuming a seurat obj. c…
Comment: Low Alignment rate by biofalconch ▴ 970
Yeap, you can sample your reads with `seqtk` like this: seqtk sample -s100 read2.fq 100 > Sample.fq Take a couple and run them throug…
Answer: obtaining circular RNAs' sequences from circBase by Barry Digby ★ 1.2k
You won't find them on circBase. circAtlas has the mature spliced sequence available. You can [search for circRNAs](https://ngdc.cncb.a…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by Ram 40k
\#TIL mambaforge - better than continuum's conda images I'm guessing?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by arriyaz.nstu ▴ 30
If the laptop doesn't support WSL2, then will the Docker (with linux) work?
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