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Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 18 months ago by ▴ 10 • written 2.2 years ago by ▴ 40
76
votes
14
replies
16k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 15 months ago by 43k • written 11.0 years ago by 9.7k
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 15 months ago by 43k • written 11.3 years ago by 6.1k
20
votes
14
replies
4.1k
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 13 months ago by 43k • written 8.0 years ago by ▴ 460
55
votes
14
replies
93k
views
10 follow
Tutorial: Using R in Conda
R
updated 14 months ago by 43k • written 3.8 years ago by ▴ 870
64
votes
13
replies
13k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 2.3 years ago by 43k • written 9.5 years ago by ★ 2.4k
35
votes
13
replies
14k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 2.3 years ago by ★ 1.4k • written 2.6 years ago by 100k
18
votes
13
replies
2.2k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 12 months ago by 43k • written 7.1 years ago by 54k
77
votes
13
replies
16k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.6 years ago by 43k • written 10.0 years ago by 20k
75
votes
13
replies
67k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 18 months ago by 43k • written 10.5 years ago by ★ 1.2k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 11 months ago by 43k • written 5.3 years ago by ▴ 170
21
votes
13
replies
11k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 6 months ago by • 0 • written 23 months ago by 82k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 9 weeks ago by • 0 • written 3.6 years ago by 3.2k
5
votes
13
replies
2.0k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 29 days ago by 82k • written 4 weeks ago by ★ 1.7k
34
votes
12
replies
30k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 14 months ago by 43k • written 10.6 years ago by 100k
8
votes
12
replies
6.8k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 13 months ago by 43k • written 8.0 years ago by 13k
6
votes
11
replies
5.7k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 15 months ago by 43k • written 7.4 years ago by ▴ 50
16
votes
11
replies
8.3k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
14 months ago by Ram 43k
12
votes
11
replies
7.6k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 12 months ago by 43k • written 7.2 years ago by ★ 2.4k
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 14 months ago by 43k • written 7.6 years ago by ★ 4.7k
6
votes
10
replies
5.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 14 months ago by 43k • written 6.2 years ago by ▴ 380
22
votes
10
replies
7.1k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 14 months ago by 43k • written 3.7 years ago by 13k
30
votes
10
replies
83k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 14 months ago by 43k • written 3.2 years ago by ★ 1.6k
16
votes
9
replies
7.2k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 23 months ago by ▴ 70 • written 2.5 years ago by ★ 1.3k
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 12 months ago by 43k • written 6.7 years ago by 88k
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 14 months ago by 43k • written 10.1 years ago by ★ 1.8k
21
votes
9
replies
6.6k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
66
votes
9
replies
49k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 15 months ago by 43k • written 10.9 years ago by ★ 3.0k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 14 months ago by 43k • written 10.1 years ago by ★ 1.9k
81
votes
8
replies
8.6k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 14 months ago by 43k • written 9.9 years ago by 20k
7
votes
8
replies
3.4k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 17 months ago by 43k • written 8.9 years ago by ★ 2.3k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 14 months ago by 43k • written 10.1 years ago by ▴ 810
99
votes
8
replies
29k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 13 months ago by 43k • written 8.2 years ago by ★ 1.1k
23
votes
8
replies
5.4k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 2.4 years ago by 43k • written 9.7 years ago by 24k
15
votes
7
replies
6.5k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 14 months ago by 43k • written 8.0 years ago by ★ 3.5k
19
votes
7
replies
6.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 months ago by 82k • written 4.2 years ago by 6.4k
12
votes
7
replies
2.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
13 months ago by barslmn ★ 2.2k
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 12 months ago by 43k • written 6.7 years ago by 88k
20
votes
7
replies
6.4k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 14 months ago by 43k • written 5.6 years ago by ▴ 800
16
votes
7
replies
16k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 14 months ago by 43k • written 4.9 years ago by ▴ 310
8
votes
7
replies
8.4k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 2.3 years ago by 43k • written 10.5 years ago by ★ 2.6k
50
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 15 months ago by 43k • written 11.7 years ago by 100k
13
votes
7
replies
6.3k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 14 months ago by 43k • written 3.7 years ago by 88k
11
votes
7
replies
12k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 12 months ago by 43k • written 3.2 years ago by ▴ 420
16
votes
6
replies
6.5k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 13 months ago by 43k • written 7.5 years ago by ★ 1.7k
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 7 weeks ago by 43k • written 6.3 years ago by 88k
61
votes
6
replies
9.5k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by 43k • written 10.8 years ago by 9.7k
30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 20 months ago by 43k • written 12.1 years ago by 100k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 14 months ago by 43k • written 10.3 years ago by 6.1k
46
votes
6
replies
25k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 2.3 years ago by ▴ 50 • written 3.2 years ago by 13k
412 results • Page 2 of 9
Recent Votes
Answer: Q: GenomeScope input and how to interpret the results
Answer: How to find tandem duplications pattern in a DNA sequence
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
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Recent Replies
Comment: GO analysis: p-value range by Matthias Zepper 4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range by marco.barr ▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range by sooni ▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values by mnx0723 • 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version) by jinyi • 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot by marco.barr ▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
Comment: Error in using BioSampleParser tool: subscript out of bounds by marco.barr ▴ 130
Hi, I also had the same problem. If you check its github page there have been no releases for many years and these errors cannot be fixed. …
Comment: Add stats to the plot by Ghada • 0
Thanks, thats really helpful ![enter image description here][1] ![enter image description here][2] [1]: /media/images/0470f3dc-5945-…
Comment: PCA Visualization error in R by marco.barr ▴ 130
SNPRelate is an R package that is able to read from VCF files directly and perform PCA and IBD/IBS. See the documentation for details in Bi…
Comment: Why most genes have high padj values by ATpoint 82k
788 differential genes is a lot. What is the problem?
Comment: Why most genes have high padj values by mnx0723 • 0
Sorry, I made edits.
Comment: Why most genes have high padj values by Pierre Lindenbaum 161k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: GO analysis: p-value range by marco.barr ▴ 130
Try adding: `scale_y_continuous(breaks=seq(0, max_count, by=0.05))`
Comment: Functional enrichment analysis for unique gene IDs by ATpoint 82k
If these genes do not have a symbol then it is utterly unlikely that anyone has looked at their function. I would get their Ensembl IDs and…
Comment: Add stats to the plot by marco.barr ▴ 130
The error is likely due to the fact that the structure of your data in data4.ts and data2.ts may not contain the Condition values. The grou…
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