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3
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0
replies
319
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Tutorial: How to make a heatmap in R and deep understand it
heatmap r
4 weeks ago by Ming Tommy Tang ★ 2.9k
34
votes
17
replies
15k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 4 weeks ago by 129k • written 9.5 years ago by 20k
2
votes
0
replies
450
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 10 weeks ago by 72k • written 10 weeks ago by ▴ 40
1
vote
0
replies
277
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
11 weeks ago by Milad ▴ 10
3
votes
2
replies
2.1k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 23 days ago by 39k • written 6.1 years ago by ▴ 100
7
votes
3
replies
1.2k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 7 weeks ago by ▴ 100 • written 9 months ago by 85k
3
votes
3
replies
1.7k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 3 months ago by 39k • written 13 months ago by ★ 3.1k
1
vote
0
replies
470
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
4 months ago by firestar ★ 1.5k
10
votes
7
replies
1.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
9 weeks ago by barslmn ★ 1.6k
1
vote
1
reply
769
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 4 months ago by 154k • written 4 months ago by ★ 1.6k
1
vote
0
replies
717
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
rRNA RNAmmer Annotation Genome
5 months ago by Dr.Animo ▴ 50
1
vote
0
replies
611
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo mining enrichment data Gene pathway RNA-Seq R
5 months ago by Novogene ▴ 300
1
vote
0
replies
737
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo mining differential data expression RNA-Seq gene R
5 months ago by Novogene ▴ 300
2
votes
0
replies
559
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo mining datasets data SRA RNA-Seq
5 months ago by Novogene ▴ 300
4
votes
0
replies
1.3k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
3 months ago by Novogene ▴ 300
49
votes
1
reply
6.6k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 3 months ago by 39k • written 2.7 years ago by 72k
1
vote
3
replies
512
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
9 weeks ago by barslmn ★ 1.6k
82
votes
21
replies
74k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by ★ 3.0k • written 4.9 years ago by ▴ 540
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 3 months ago by 39k • written 7.2 years ago by 20k
12
votes
31
replies
5.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 12 weeks ago by 39k • written 3.8 years ago by 7.9k
1
vote
2
replies
740
views
Tutorial: ViennaRNA package installation in Windows
install mfold viennarna rna windows
updated 8 months ago by 9.6k • written 8 months ago by ▴ 20
1
vote
0
replies
403
views
Tutorial: Making LDA Score plot
LDA metagenomics
8 months ago by rohitsatyam102 ▴ 690
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 10 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
11
votes
7
replies
7.3k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 16 days ago by 39k • written 2.3 years ago by ▴ 300
12
votes
1
reply
2.6k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 9 months ago by ★ 1.8k • written 17 months ago by 14k
14
votes
9
replies
4.2k
views
6 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 4 weeks ago by • 0 • written 11 months ago by 72k
83
votes
21
replies
16k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 12 weeks ago by 39k • written 2.6 years ago by 2.9k
27
votes
0
replies
2.9k
views
Tutorial: Building Docker images
singularity docker container
10 months ago by ATpoint 72k
1
vote
1
reply
27k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 10 months ago by ★ 2.9k • written 10 months ago by ▴ 10
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 8 days ago by • 0 • written 5.0 years ago by ★ 1.3k
80
votes
2
replies
54k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 3 months ago by 39k • written 9.9 years ago by 11k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 12 weeks ago by 39k • written 5.5 years ago by ▴ 750
38
votes
8
replies
10k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 12 weeks ago by 39k • written 2.7 years ago by 2.9k
3
votes
2
replies
1.6k
views
Tutorial: Running fastq_screen on your data
fastqscreen
14 months ago by rohitsatyam102 ▴ 690
7
votes
14
replies
2.4k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 7 months ago by • 0 • written 15 months ago by ▴ 30
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
27
votes
13
replies
8.2k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 16 months ago by ★ 1.2k • written 19 months ago by 98k
3
votes
13
replies
10k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 12 weeks ago by 39k • written 4.3 years ago by ▴ 140
16
votes
9
replies
4.6k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 11 months ago by ▴ 70 • written 18 months ago by ★ 1.1k
2
votes
0
replies
1.2k
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
updated 4 days ago by 39k • written 17 months ago by ▴ 20
0
votes
0
replies
9.3k
views
Tutorial: Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter Python pattern
17 months ago by Wayne ★ 1.8k
12
votes
4
replies
4.7k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 3 months ago by 39k • written 2.3 years ago by ▴ 120
26
votes
10
replies
63k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 12 weeks ago by 39k • written 2.2 years ago by ★ 1.3k
6
votes
2
replies
2.9k
views
Tutorial: Unsupervised clustering on gene expression data
gene RNA-seq expression clustering
8 months ago by Hamid Ghaedi 2.9k
42
votes
6
replies
19k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 16 months ago by ▴ 40 • written 2.2 years ago by 12k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 weeks ago by ▴ 10 • written 5.5 years ago by 85k
15
votes
2
replies
1.6k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 7 months ago by ▴ 810 • written 20 months ago by ▴ 280
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 4 months ago by 39k • written 10.7 years ago by 20k
6
votes
2
replies
1.1k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
21 months ago by Kevin Blighe 85k
356 results • Page 1 of 8
Recent Votes
How to make the profile line of `deepTools::plotHeatmap` more smooth?
Answer: How to make the profile line of `deepTools::plotHeatmap` more smooth?
Comment: Getting species names and taxa id from assembly accession number
Comment: STAR GenomeIndex output (which is the BAM file?)
Answer: [Meta] Use of AI
Answer: h5ad cellxgene to R
Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
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Popular Question to benformatics 3.6k
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Recent Replies
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental by Kevin Blighe 85k
Hello friend. Life moves on...
Comment: How to make the profile line of `deepTools::plotHeatmap` more smooth? by Dan ▴ 120
Do you mean I should check the intersections between the peaks in the `bed` file using `bedtools intersect` (https://bedtools.readthedocs.i…
Answer: How to make the profile line of `deepTools::plotHeatmap` more smooth? by Trivas ★ 1.2k
Your issue is with your bed file then, not necessarily with deep tools. I'd look into the bedtools suite to see if you can minimize overlap…
Comment: variant allelic fraction by Pierre Lindenbaum 154k
https://www.biostars.org/p/492331/
Comment: variant allelic fraction by malm • 0
ok how can i calculate it from the vep file?
Comment: Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads by benformatics 3.6k
I think it would be fair (and conservative) to remove read pairs where one maps to the mitochondrial genome. It should be a relatively very…
Answer: Convert Bam file to Fastq by Michael 52k
I think your code is incorrect bash syntax. I think you want something like this: sort bam_headers.txt > bam_haeders-sorted.txt # c…
Comment: Combination of ROC CURVE by Maria17 ▴ 20
For example, if three targets are combined and the mean value is plotted, the different combinations give different numbers, but there are …
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental by Kermit ▴ 80
neither simple nor helpful, but perhaps the OP changed his question away from "why might diff models produce diff results" to the current "…
Comment: Convert Bam file to Fastq by Michael 52k
At first, I would trust samtools to do the right thing but of course it doesn't hurt to double check. But I think the crux is what is in fa…
Comment: Convert Bam file to Fastq by Pierre Lindenbaum 154k
paste fastq1_read_ids.txt fastq2_read_ids.txt is a tabular file with two column. Is it the same for bam_read_names.txt ?
Comment: variant allelic fraction by Pierre Lindenbaum 154k
this is not a field provided by VEP.
Answer: WGCNA Trait File Issues by Jennifer M • 0
![enter image description here][1] [1]: /media/images/0cf4eaa7-9550-4bbb-b43e-208dc787
Comment: Pairwise Alignment by WouterDeCoster 47k
> for whole genome analysis What do you mean with that? You provide too little information for us to answer your question.
Comment: Getting species names and taxa id from assembly accession number by GenoMax 129k
There must be some temporary glitch. Following command works (via EntrezDirect): $ esearch -db assembly -query GCA_000001405.29 | esu…
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