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31
votes
6
replies
11k
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Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 6 months ago by 40k • written 3.4 years ago by 86k
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
20
votes
6
replies
5.2k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 6 months ago by 40k • written 7.0 years ago by ★ 5.2k
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
39
votes
6
replies
18k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 4 months ago by 40k • written 6.1 years ago by ★ 3.3k
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
54
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 12 months ago by 40k • written 9.8 years ago by ★ 1.2k
5
votes
5
replies
6.5k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 4 months ago by 40k • written 5.9 years ago by ▴ 130
2
votes
5
replies
2.0k
views
Tutorial: Building OMA database on SGE
oma
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
16
votes
5
replies
8.7k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 7 months ago by 40k • written 11.0 years ago by 20k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 6 months ago by 40k • written 5.8 years ago by ▴ 760
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 17 months ago by 40k • written 9.5 years ago by ★ 1.8k
64
votes
5
replies
7.0k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 11 months ago by 40k • written 8.1 years ago by 12k
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 6 months ago by 40k • written 5.2 years ago by ★ 9.3k
20
votes
5
replies
6.5k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 5 months ago by 40k • written 7.2 years ago by ★ 1.5k
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 5 months ago by 40k • written 7.3 years ago by 20k
36
votes
5
replies
5.8k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 18 days ago by ▴ 20 • written 8.2 years ago by ▴ 410
9
votes
5
replies
2.1k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 4 months ago by 40k • written 6.2 years ago by 98k
12
votes
5
replies
7.9k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 5 months ago by 40k • written 7.3 years ago by ★ 9.3k
29
votes
5
replies
6.1k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 6 months ago by 40k • written 10.0 years ago by ★ 4.3k
12
votes
5
replies
2.1k
views
Tutorial: FASTA file split
fasta
updated 6 months ago by 40k • written 3.3 years ago by 8.2k
15
votes
4
replies
4.3k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 330
10
votes
4
replies
10k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 6 months ago by 40k • written 4.2 years ago by 5.5k
20
votes
4
replies
2.4k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 6 months ago by 40k • written 4.4 years ago by ▴ 180
24
votes
4
replies
6.9k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 6 months ago by 40k • written 4.1 years ago by 76k
32
votes
4
replies
7.0k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 6 months ago by 40k • written 4.9 years ago by ★ 1.6k
3
votes
4
replies
3.5k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 4 months ago by 40k • written 4.9 years ago by ▴ 340
9
votes
4
replies
4.0k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
6 weeks ago by Hamid Ghaedi 3.0k
3
votes
4
replies
4.2k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 4 months ago by 40k • written 5.4 years ago by ★ 2.4k
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 5 months ago by 40k • written 7.0 years ago by ★ 4.2k
6
votes
4
replies
7.2k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 7 months ago by 40k • written 10.5 years ago by 11k
19
votes
4
replies
8.6k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 7 months ago by 40k • written 10.6 years ago by 98k
10
votes
4
replies
3.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 4 months ago by 40k • written 5.6 years ago by 86k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 7 months ago by 40k • written 10.5 years ago by 20k
1
vote
4
replies
3.1k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
28
votes
4
replies
4.1k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 6 months ago by 40k • written 4.7 years ago by 26k
12
votes
4
replies
2.0k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 6 months ago by 40k • written 6.0 years ago by ▴ 590
12
votes
4
replies
5.0k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 7 months ago by 40k • written 2.6 years ago by ▴ 130
1
vote
4
replies
3.1k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 4 months ago by 40k • written 5.4 years ago by ▴ 340
2
votes
3
replies
2.5k
views
Tutorial: It's about the journey, and not the destination
R network
updated 4 months ago by 40k • written 6.5 years ago by ★ 1.2k
1
vote
3
replies
688
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
6 months ago by barslmn ★ 1.8k
0
votes
3
replies
50k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
5
votes
3
replies
4.0k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 7 months ago by 40k • written 10.8 years ago by ▴ 80
5
votes
3
replies
5.0k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 6 months ago by • 0 • written 5.9 years ago by ▴ 130
19
votes
3
replies
13k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 14 months ago by 40k • written 7.6 years ago by ★ 9.3k
3
votes
3
replies
2.2k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 7 months ago by 40k • written 17 months ago by ★ 3.3k
72
votes
3
replies
36k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 22 months ago by 40k • written 9.2 years ago by 98k
13
votes
3
replies
11k
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 5 weeks ago by ▴ 20 • written 6.5 years ago by ★ 1.6k
7
votes
3
replies
1.7k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 5 months ago by ▴ 110 • written 13 months ago by 86k
11
votes
3
replies
1.3k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 5 months ago by 40k • written 7.2 years ago by 7.1k
379 results • Page 3 of 8
Recent Votes
Comment: Calculation of TMB on gene level
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
Answer: Filter transcription factors
Comment: Quantification after transcriptome assembly with Trinity
Snakemake: output folder a as dependency to a different rule
A: Snakemake: output folder a as dependency to a different rule
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
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Recent Replies
Comment: bcftools error merging two VCFs: REF prefixes differ by iraun 6.1k
I can't find information with respect to the reference genome used to call the variants in `VCF_d`, but in `VCF_p` it seems they used GRCh3…
Comment: Calculation of TMB on gene level by smrutimayipanda ▴ 20
I am asking about TMB calculation on gene level, especially TCGA data
Comment: Calculation of TMB on gene level by smrutimayipanda ▴ 20
can you please tell me why it is technically incorrect?
Answer: Gene enrichment analysis of prokaryotes gene by dthorbur ▴ 550
[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses. [H…
Comment: Read block operation failed with BAM file by John Marshall 3.0k
Indeed, though it is a seek issue when accessing files **over HTTP and other network protocols**. So, unless there's something you didn't m…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by RM123 ▴ 10
Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
Comment: gene correlations in between two groups by ATpoint 76k
And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details. …
Comment: gene correlations in between two groups by edus_bioinfo ▴ 40
Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype by dthorbur ▴ 550
Hello again. Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by RM123 ▴ 10
Hello Dariober, That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R by Nicolas Rosewick 10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting by fracarb8 ★ 1.2k
You did not add the screenshot.
Answer: BED files by Alex Reynolds 35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by dariober 14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files by barslmn ★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
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