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Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 8 months ago by 41k • written 4.9 years ago by 78k
49
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
48
votes
30
replies
9.3k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 4 weeks ago by 78k • written 7.7 years ago by 41k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 10 months ago by 41k • written 10.8 years ago by 99k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 9 months ago by 41k • written 11.7 years ago by ▴ 540
44
votes
6
replies
22k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 22 months ago by ▴ 40 • written 2.7 years ago by 12k
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 7 months ago by 41k • written 7.7 years ago by ★ 3.2k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 9 months ago by 41k • written 9.8 years ago by 6.0k
42
votes
16
replies
23k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 15 months ago by 41k • written 8.2 years ago by ★ 2.4k
42
votes
19
replies
7.6k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 9 months ago by 41k • written 10.8 years ago by 4.1k
42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 9 months ago by 41k • written 9.6 years ago by ★ 1.9k
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
39
votes
6
replies
18k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 6 months ago by 41k • written 6.3 years ago by ★ 3.4k
36
votes
5
replies
5.9k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 12 weeks ago by ▴ 20 • written 8.4 years ago by ▴ 410
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 25 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
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 7 months ago by 136k • written 10.0 years ago by 20k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 months ago by 41k • written 7.2 years ago by ▴ 310
34
votes
15
replies
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
32
votes
12
replies
29k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 9 months ago by 41k • written 10.1 years ago by 99k
32
votes
4
replies
7.3k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 8 months ago by 41k • written 5.1 years ago by ★ 1.6k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 8 months ago by 41k • written 3.5 years ago by 86k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 9 months ago by 41k • written 9.6 years ago by ▴ 810
30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 14 months ago by 41k • written 11.6 years ago by 99k
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 9 months ago by 41k • written 10.8 years ago by 6.0k
29
votes
5
replies
6.2k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 9 months ago by 41k • written 10.2 years ago by ★ 4.4k
29
votes
10
replies
73k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 8 months ago by 41k • written 2.7 years ago by ★ 1.5k
28
votes
13
replies
12k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 22 months ago by ★ 1.3k • written 2.1 years ago by 99k
28
votes
4
replies
4.1k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 8 months ago by 41k • written 4.9 years ago by 26k
27
votes
0
replies
3.4k
views
Tutorial: Building Docker images
singularity docker container
16 months ago by ATpoint 78k
26
votes
17
replies
7.3k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 14 months ago by 41k • written 9.3 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 8 months ago by 41k • written 4.1 years ago by 19k
25
votes
15
replies
8.6k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 9 months ago by 41k • written 10.9 years ago by 9.7k
24
votes
4
replies
7.1k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 8 months ago by 41k • written 4.3 years ago by 78k
23
votes
8
replies
5.2k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 23 months ago by 41k • written 9.3 years ago by 24k
23
votes
19
replies
6.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 7 months ago by 41k • written 7.2 years ago by ★ 2.5k
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 7 months ago by 41k • written 7.1 years ago by ★ 2.1k
22
votes
1
reply
3.1k
views
Tutorial: Introduction To R Course Materials Available
R
updated 11 months ago by 41k • written 11.6 years ago by 26k
21
votes
2
replies
5.1k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 14 months ago by ▴ 40 • written 2.6 years ago by 8.4k
21
votes
9
replies
6.3k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
21
votes
5
replies
6.6k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 7 months ago by 41k • written 7.4 years ago by ★ 1.5k
21
votes
10
replies
6.3k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 8 months ago by 41k • written 3.2 years ago by 12k
20
votes
14
replies
3.7k
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 7 months ago by 41k • written 7.6 years ago by ▴ 460
20
votes
0
replies
8.6k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 7 months ago by 41k • written 7.2 years ago by ★ 4.2k
20
votes
2
replies
7.7k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.4k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 9 months ago by 41k • written 10.7 years ago by 20k
20
votes
4
replies
2.5k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 8 months ago by 41k • written 4.6 years ago by ▴ 180
20
votes
6
replies
5.3k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 8 months ago by 41k • written 7.2 years ago by ★ 5.2k
20
votes
7
replies
6.1k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 8 months ago by 41k • written 5.1 years ago by ▴ 770
383 results • Page 2 of 8
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
Comment: Merging FASTQ files with Cellranger
Finding human .vcf files online to download
Answer: Should I scale all genes in single cell Seurat?
Answer: Should I scale all genes in single cell Seurat?
Answer: Should I scale all genes in single cell Seurat?
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Recent Replies
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements? by cmdcolin ★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations by Jordan M Eizenga ▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ? by Jordan M Eizenga ▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ? by Brian Bushnell 19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data by Tm ★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them? by Brian Bushnell 19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download by cmdcolin ★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization by m.habib • 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by jv ★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands? by Malachi Griffith 19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
Answer: How Can I move the scattered dots more closer into the center of box ? by Trivas ★ 1.5k
You added a position dodge on your boxplot but not on your points.
Comment: How Can I move the scattered dots more closer into the center of box ? by ATpoint 78k
Please understand that biostars is not a helpdesk for trivial ggplot questions. Google it and find help on previous StackExchange sites, or…
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by jucosie • 0
Hello, I am reviewing some old scripts in which I used clumpify.sh (BBMap 38.90) with the following parameters: ./clumpify.sh in1=$d…
Comment: Problematic fastq files...How can we trust them? by Istvan Albert 99k
perhaps ask her about the origin of the data, how was the data postprocessed FASTQ data is a bit more resilient than other types of data a…
Answer: GO categorization by Istvan Albert 99k
If you have an organism that lacks the GO to gene mapping then you have to find a way to assign these terms to your genes. Basically your …
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