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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
50
votes
14
replies
74k
views
10 follow
Tutorial: Using R in Conda
R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 750
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
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 months ago by 40k • written 10.4 years ago by 9.7k
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
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 19 months ago by 40k • written 8.9 years ago by ★ 2.4k
75
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 10 months ago by 40k • written 9.8 years ago by ★ 1.2k
18
votes
13
replies
6.7k
views
9 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 10 weeks ago by 53k • written 15 months ago by 76k
76
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 23 months ago by 40k • written 9.3 years ago by 19k
17
votes
13
replies
1.9k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 4 months ago by 40k • written 6.5 years ago by 53k
4
votes
13
replies
11k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 3 months ago by 40k • written 4.6 years ago by ▴ 140
8
votes
12
replies
6.4k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 5 months ago by 40k • written 7.3 years ago by 13k
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
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 6 months ago by 40k • written 6.9 years ago by ★ 4.7k
16
votes
11
replies
7.7k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
6 months ago by Ram 40k
12
votes
11
replies
7.0k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 4 months ago by 40k • written 6.5 years ago by ★ 2.4k
6
votes
11
replies
5.1k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 7 months ago by 40k • written 6.8 years ago by ▴ 50
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
6
votes
10
replies
4.8k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 6 months ago by 40k • written 5.6 years ago by ▴ 370
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
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
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 months ago by 40k • written 10.2 years ago by ★ 3.0k
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
9
votes
9
replies
3.9k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 4 months ago by 40k • written 6.0 years ago by 86k
21
votes
9
replies
6.2k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 6 months ago by 40k • written 10.3 years ago by 9.7k
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 6 months ago by 40k • written 9.4 years ago by ★ 1.8k
16
votes
9
replies
5.8k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 15 months ago by ▴ 70 • written 22 months ago by ★ 1.2k
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
7
votes
8
replies
3.2k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 9 months ago by 40k • written 8.2 years ago by ★ 2.2k
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
81
votes
8
replies
8.1k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 6 months ago by 40k • written 9.3 years ago by 19k
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 5 months ago by 40k • written 7.6 years ago by ★ 1.1k
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
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
8
votes
7
replies
8.0k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 19 months ago by 40k • written 9.8 years ago by ★ 2.6k
16
votes
7
replies
14k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 6 months ago by 40k • written 4.3 years ago by ▴ 310
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
11
votes
7
replies
9.1k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 4 months ago by 40k • written 2.6 years ago by ▴ 350
14
votes
7
replies
5.9k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 6 months ago by 40k • written 7.4 years ago by ★ 3.3k
11
votes
7
replies
1.7k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
5 months ago by barslmn ★ 1.8k
12
votes
7
replies
5.3k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 6 months ago by 40k • written 3.0 years ago by 86k
18
votes
7
replies
5.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 9 weeks ago by 76k • written 3.5 years ago by 5.5k
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 4 months ago by 40k • written 6.0 years ago by 86k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 6 months ago by 40k • written 5.1 years ago by 16k
16
votes
6
replies
6.1k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 5 months ago by 40k • written 6.9 years ago by ★ 1.7k
13
votes
6
replies
5.5k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 5 months ago by 40k • written 7.3 years ago by 14k
11
votes
6
replies
4.7k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 14 months ago by 40k • written 7.6 years ago by ★ 4.2k
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
2
votes
6
replies
2.9k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 5 months ago by 40k • written 7.2 years ago by ▴ 140
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
379 results • Page 2 of 8
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Concatenating fastq.gz files across lanes
A: Concatenating fastq.gz files across lanes
Answer: bedGraph for Coverage of Insert from Paired-End Data?
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
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Recent Replies
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 ▴ 960
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?
Comment: Integrated Seurat object change name of the two conditions by camillab. ▴ 130
thanks but my metadata looks different from yours. Will it work even there are not the same "structure"? or…
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool? by ATpoint 76k
Docker is great, I use it daily since you're independent of the host computer and can share and pull the images via DockerHub. It's also gr…
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact? by ATpoint 76k
If you do DE analysis on single-cell level then I find it critical to enforce some cutoff, as many cells means a lot of power so you get ev…
Comment: Visualize where kmers are on a reference genome by Ram 40k
Did you google "visualize BED file on genome"?<a href="" title="Text added because biostars parser needs it"></a>
Comment: obtaining circular RNAs' sequences from circBase by Ram 40k
> as you know No I did not. I know this is a cultural mannerism but it's antiquated. Please abandon this phrase, it can come across as con…
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact? by omer.shomrat • 0
Thanks a lot for the response! I'm doing pathway enrichment analysis (using clusterProfiler) on almost all genes in each cluster, with the…
Comment: Unable to build applet in DNAnexus, .jar file not found by Ram 40k
Ah I missed the part where DNANexus makes this problem out of our reach. Thank you, GenoMax!
Answer: Unable to build applet in DNAnexus, .jar file not found by Ram 40k
That's not how `$PATH` works. Place your jar file in any accessible location, then add a script to your `/usr/local/bin` like so: ``` #…
Comment: Unable to build applet in DNAnexus, .jar file not found by GenoMax 134k
Please contact DNANexus support. That may be your best bet since this is commercial software and not many here will have access.
Comment: How to determine the total count for each gene in lymphotype B by fracarb8 ★ 1.2k
A quick way is # select only B cells Idents(rds_obj) <- "clusters" rds_obj <- subset(rds_obj, idents = "lymphocyte B", invert…
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