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7
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14
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2.9k
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6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 11 months ago by • 0 • written 19 months ago by ▴ 30
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
11
votes
7
replies
1.7k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
5 months ago by barslmn ★ 1.8k
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
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
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
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
61
votes
6
replies
9.2k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 6 months ago by 40k • written 10.1 years ago by 9.7k
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
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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Comment: I have performed Trimmomatic run for adapter removal. QC report shows drop in th by swbarnes2 13k
The library is non-existent? The reagents got fried? The instrument failed? All of those will affect the assembly processes in a profoun…
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?
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