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Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 17 months ago by ▴ 10 • written 2.1 years ago by ▴ 40
54
votes
14
replies
91k
views
10 follow
Tutorial: Using R in Conda
R
updated 13 months ago by 43k • written 3.7 years ago by ▴ 840
76
votes
14
replies
16k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
20
votes
14
replies
4.0k
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 12 months ago by 43k • written 7.9 years ago by ▴ 460
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 13 months ago by 43k • written 11.2 years ago by 6.0k
21
votes
13
replies
10k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 months ago by • 0 • written 22 months ago by 81k
35
votes
13
replies
14k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 2.2 years ago by ★ 1.4k • written 2.5 years ago by 100k
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 17 months ago by 43k • written 10.4 years ago by ★ 1.2k
18
votes
13
replies
2.2k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 11 months ago by 43k • written 7.1 years ago by 54k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 10 months ago by 43k • written 5.2 years ago by ▴ 170
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 2.2 years ago by 43k • written 9.4 years ago by ★ 2.4k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 5 weeks ago by • 0 • written 3.5 years ago by 3.2k
77
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.5 years ago by 43k • written 9.9 years ago by 19k
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 13 months ago by 43k • written 10.5 years ago by 100k
8
votes
12
replies
6.7k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 12 months ago by 43k • written 7.9 years ago by 13k
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 13 months ago by 43k • written 7.5 years ago by ★ 4.7k
6
votes
11
replies
5.7k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 14 months ago by 43k • written 7.3 years ago by ▴ 50
16
votes
11
replies
8.2k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
13 months ago by Ram 43k
12
votes
11
replies
7.5k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 11 months ago by 43k • written 7.1 years ago by ★ 2.4k
30
votes
10
replies
81k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 13 months ago by 43k • written 3.1 years ago by ★ 1.6k
22
votes
10
replies
7.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 13 months ago by 43k • written 3.6 years ago by 13k
6
votes
10
replies
5.2k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 13 months ago by 43k • written 6.1 years ago by ▴ 370
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 11 months ago by 43k • written 6.6 years ago by 87k
21
votes
9
replies
6.5k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 13 months ago by 43k • written 10.9 years ago by 9.7k
16
votes
9
replies
7.0k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 22 months ago by ▴ 70 • written 2.4 years ago by ★ 1.3k
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 13 months ago by 43k • written 10.0 years ago by ★ 1.8k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 13 months ago by 43k • written 10.0 years ago by ★ 1.9k
66
votes
9
replies
49k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 14 months ago by 43k • written 10.8 years ago by ★ 3.0k
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 16 months ago by 43k • written 8.8 years ago by ★ 2.3k
99
votes
8
replies
29k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 12 months ago by 43k • written 8.1 years ago by ★ 1.1k
81
votes
8
replies
8.5k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 13 months ago by 43k • written 9.9 years ago by 19k
23
votes
8
replies
5.4k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 2.3 years ago by 43k • written 9.6 years ago by 24k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 13 months ago by 43k • written 10.0 years ago by ▴ 810
50
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 14 months ago by 43k • written 11.6 years ago by 100k
13
votes
7
replies
6.1k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 13 months ago by 43k • written 3.6 years ago by 87k
11
votes
7
replies
2.2k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
12 months ago by barslmn ★ 2.1k
20
votes
7
replies
6.3k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 13 months ago by 43k • written 5.5 years ago by ▴ 800
8
votes
7
replies
8.3k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 2.2 years ago by 43k • written 10.4 years ago by ★ 2.6k
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 11 months ago by 43k • written 6.6 years ago by 87k
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 11 months ago by 43k • written 3.1 years ago by ▴ 410
16
votes
7
replies
16k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 13 months ago by 43k • written 4.8 years ago by ▴ 310
15
votes
7
replies
6.4k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 13 months ago by 43k • written 7.9 years ago by ★ 3.5k
19
votes
7
replies
6.5k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 9 months ago by 81k • written 4.1 years ago by 6.3k
44
votes
6
replies
24k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 2.2 years ago by ▴ 40 • written 3.1 years ago by 13k
32
votes
6
replies
12k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 13 months ago by 43k • written 3.9 years ago by 87k
2
votes
6
replies
3.1k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 12 months ago by 43k • written 7.8 years ago by ▴ 140
16
votes
6
replies
6.4k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 12 months ago by 43k • written 7.5 years ago by ★ 1.7k
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 22 days ago by 43k • written 6.2 years ago by 87k
106
votes
6
replies
26k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 13 months ago by 43k • written 5.6 years ago by 16k
67
votes
6
replies
26k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 14 months ago by 43k • written 11.6 years ago by 100k
409 results • Page 2 of 9
Recent Votes
How to comparing two bacterial genomes and find the mutation, rearrangement etc.
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: Korean reference file
How to get all genes for a specific list of regions in R preferably using Biomart
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: Sheep reference genome remapping coordinates
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Recent Replies
Answer: change gene IDs to gene name in RNAseq by Trivas ★ 1.7k
This has been answered a million times on this forum, see here https://www.biostars.org/p/430015/
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome by colindaven 6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by Elisabeth Gasteiger ★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates by valentinatsar • 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies by GenoMax 141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file by GenoMax 141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR by GenoMax 141k
> But it keeps giving error Please tell us what the error is.
Answer: 10x VDJ (TCR/BCR) BAM to fastq by GenoMax 141k
Looking at the information about the BAM file in the link included at the end of this sentence, it seems that the BAM file does not contain…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by Jacky • 0
I got it, thank you for your response.
Answer: DEseq2 by ATpoint 81k
The DESeq2 input is a numeric count matrix (or data.frame) with rows being genes/observations and columns being samples/cells/specimen. Ple…
Comment: How to add motifs in cellranger-arc reference? by Ehsan • 0
Hi. Do you have any updates on what you ended up doing? I am encountering same issue, cannot really find a good TF motif database for zebra…
Comment: biomaRt error for different R version by manaswwm ▴ 490
Wonderful, and thanks for tagging Mike! For those who come back for this problem, the following seemed to work for me: Downgrading `dbply…
Answer: Assume "yes" as the answer to any prompts with bioconda by Juke34 8.5k
From my experience using `biocontainers` base container no need to set `yes` installation is done without any command prompt, otherwise as …
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