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412 results • Page 3 of 9
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20
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6
replies
5.7k
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Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 14 months ago by 43k • written 7.7 years ago by ★ 5.2k
12
votes
6
replies
5.0k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 22 months ago by 43k • written 8.3 years ago by ★ 4.3k
32
votes
6
replies
12k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 14 months ago by 43k • written 4.0 years ago by 88k
13
votes
6
replies
6.0k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 13 months ago by 43k • written 7.9 years ago by 14k
2
votes
6
replies
3.2k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 13 months ago by 43k • written 7.9 years ago by ▴ 140
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
67
votes
6
replies
26k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 15 months ago by 43k • written 11.7 years ago by 100k
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
16
votes
5
replies
9.0k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 15 months ago by 43k • written 11.7 years ago by 20k
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 2.1 years ago by 43k • written 10.1 years ago by ★ 1.8k
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 8 months ago by ▴ 20 • written 8.8 years ago by ▴ 430
12
votes
5
replies
2.5k
views
Tutorial: FASTA file split
fasta
updated 14 months ago by 43k • written 3.9 years ago by 8.6k
21
votes
5
replies
6.8k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 13 months ago by 43k • written 7.9 years ago by ★ 1.5k
10
votes
5
replies
24k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 14 months ago by 43k • written 5.8 years ago by ★ 9.4k
29
votes
5
replies
6.4k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 14 months ago by 43k • written 10.7 years ago by ★ 4.4k
6
votes
5
replies
7.0k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 12 months ago by 43k • written 6.5 years ago by ▴ 140
64
votes
5
replies
7.3k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 19 months ago by 43k • written 8.8 years ago by 12k
2
votes
5
replies
2.2k
views
Tutorial: Building OMA database on SGE
oma
updated 13 months ago by 43k • written 7.9 years ago by ▴ 10
5
votes
5
replies
668
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 14 days ago by • 0 • written 22 days ago by ★ 3.9k
16
votes
5
replies
13k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 14 months ago by 43k • written 6.5 years ago by ▴ 800
54
votes
5
replies
15k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 19 months ago by 43k • written 10.5 years ago by ★ 1.2k
9
votes
5
replies
2.3k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 12 months ago by 43k • written 6.9 years ago by 100k
1
vote
5
replies
668
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
12
votes
5
replies
8.4k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 13 months ago by 43k • written 8.0 years ago by ★ 9.4k
15
votes
5
replies
16k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 13 months ago by 43k • written 7.9 years ago by 20k
19
votes
4
replies
8.9k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 14 months ago by 43k • written 11.2 years ago by 100k
15
votes
4
replies
4.6k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 14 months ago by 43k • written 3.8 years ago by ▴ 340
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 14 months ago by 43k • written 11.2 years ago by 20k
3
votes
4
replies
4.5k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 12 months ago by 43k • written 6.0 years ago by ★ 2.5k
1
vote
4
replies
3.5k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 13 months ago by 43k • written 7.9 years ago by ▴ 10
32
votes
4
replies
8.0k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 14 months ago by 43k • written 5.5 years ago by ★ 1.6k
1
vote
4
replies
3.4k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 12 months ago by 43k • written 6.0 years ago by ▴ 340
24
votes
4
replies
7.7k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 14 months ago by 43k • written 4.8 years ago by 82k
12
votes
4
replies
5.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 15 months ago by 43k • written 3.3 years ago by ▴ 130
0
votes
4
replies
773
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
6 months ago by Coremine Medical ▴ 20
12
votes
4
replies
2.2k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 14 months ago by 43k • written 6.7 years ago by ▴ 590
20
votes
4
replies
2.7k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 14 months ago by 43k • written 5.0 years ago by ▴ 180
10
votes
4
replies
5.7k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
9 months ago by Hamid Ghaedi 3.2k
10
votes
4
replies
11k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 14 months ago by 43k • written 4.9 years ago by 6.4k
29
votes
4
replies
4.5k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 14 months ago by 43k • written 5.3 years ago by 27k
20
votes
4
replies
8.6k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 13 months ago by 43k • written 7.7 years ago by ★ 4.3k
6
votes
4
replies
7.5k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 14 months ago by 43k • written 11.2 years ago by 11k
3
votes
4
replies
3.6k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 11 months ago by 43k • written 5.6 years ago by ▴ 340
75
votes
3
replies
39k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 2.5 years ago by 43k • written 9.8 years ago by 100k
5
votes
3
replies
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 14 months ago by 43k • written 11.5 years ago by ▴ 80
8
votes
3
replies
2.8k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 22 months ago by 43k • written 8.3 years ago by 23k
1
vote
3
replies
975
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
13 months ago by barslmn ★ 2.2k
4
votes
3
replies
4.6k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 14 months ago by 43k • written 6.1 years ago by ★ 4.0k
14
votes
3
replies
20k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 9 months ago by ▴ 30 • written 7.1 years ago by ★ 1.6k
2
votes
3
replies
648
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
412 results • Page 3 of 9
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Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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Recent Replies
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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