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Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
3 days ago by Coremine Medical ▴ 10
1
vote
0
replies
124
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 3 days ago by 39k • written 3 days ago by ▴ 10
3
votes
0
replies
337
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
5 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 5 weeks ago by 130k • written 9.6 years ago by 20k
2
votes
0
replies
472
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 11 weeks ago by 73k • written 11 weeks ago by ▴ 40
1
vote
0
replies
289
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
12 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 27 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 8 weeks ago by ▴ 100 • written 10 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 14 months ago by ★ 3.1k
1
vote
0
replies
479
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
1.4k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
10 weeks ago by barslmn ★ 1.6k
1
vote
1
reply
798
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 4 months ago by 155k • written 4 months ago by ★ 1.6k
1
vote
0
replies
741
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
626
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
752
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
569
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 73k
1
vote
3
replies
519
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
10 weeks ago by barslmn ★ 1.6k
82
votes
21
replies
75k
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 3 months ago by 39k • written 3.8 years ago by 7.9k
1
vote
2
replies
757
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
417
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 11 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
11
votes
7
replies
7.4k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 20 days ago by 39k • written 2.3 years ago by ▴ 300
14
votes
1
reply
2.7k
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
4.4k
views
6 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 5 weeks ago by • 0 • written 11 months ago by 73k
83
votes
21
replies
16k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 3 months 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 73k
1
vote
1
reply
28k
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 13 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 10.0 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 3 months 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 3 months ago by 39k • written 2.7 years ago by 2.9k
3
votes
2
replies
1.7k
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 4 months ago by 39k • written 10.1 years ago by 9.6k
27
votes
13
replies
8.3k
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 20 months ago by 98k
3
votes
13
replies
10k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 3 months ago by 39k • written 4.3 years ago by ▴ 140
16
votes
9
replies
4.7k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 12 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 8 days ago by 39k • written 17 months ago by ▴ 20
0
votes
0
replies
9.5k
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 4 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 3 months 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
358 results • Page 1 of 8
Recent Votes
Tools To Calculate Average Coverage For A Bam File?
Comment: conda: command not found: gatk.
Answer: Finding Enhancers using Genomation library
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
Answer: Extract variants/SNPs with T>G substitution from a VCF file
Comment: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
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Popular Question to nishimalhotra2612 ▴ 50
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Comment: Can I send my PyMol results to a web-page as a result for a submitted query? If by Aatif Hashmi • 0
Basically I only want to show bases with disulphide bonds. like imagine I have a disulphide bond at 68 cys residue along with 145 cys. I …
Answer: How do I specify the Recalibration_data.table for "PrintReads" in GATK 4.3, if t by Pierre Lindenbaum 155k
do you want ApplyBQSR "Apply base quality score recalibration " ? https://gatk.broadinstitute.org/hc/en-us/articles/360036856671-ApplyBQSR
Answer: target vs. bait BED files for Illumina WES by Sounkou-bioinfo • 0
Hi @jacorvar , did you find the answer to that question ?
Comment: ChatGPT optimized for bioinformatics questions by Dr William Klubinski ▴ 100
That's an excellent point. A significant number of students are engaged in academic misconduct due to the use of fabricated references and …
Comment: Filtering content in heatmap to highest values by Papyrus ★ 2.5k
You mean something like this? depends on how you define "top" row or column # Create example (it is a data.table) ListerTFHeat <- …
Comment: conda: command not found: gatk. by 666billgaytes ▴ 10
Could there be an issue with your OS? I find a lot of colleagues having problems with Mac OS and much less if none at all on Windows.
Comment: ChatGPT optimized for bioinformatics questions by Dr William Klubinski ▴ 100
Great initiative :D
Answer: Extract variants/SNPs with T>G substitution from a VCF file by 4galaxy77 2.7k
Use ```bcftools view``` with the `-i` flag for including variants. ``` bcftools view -i'REF=="T" & AlT == "G"' ```
Comment: A question about the raw RNA-seq processing workflow by Dr William Klubinski ▴ 100
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity by Ben_Ensembl ★ 2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post: https://www.ensembl.inf…
Comment: conda: command not found: gatk. by bestone ▴ 20
Is there anyone who can help me with this?
Comment: conda: command not found: gatk. by bestone ▴ 20
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
Comment: conda: command not found: gatk. by Pierre Lindenbaum 155k
> how about all your previous questions ? take a time to validate the good answers
Comment: conda: command not found: gatk. by bestone ▴ 20
I was using gatk before, but conda env create -n gatk -f gatkcondaenv.yml didn't run this command, so I wanted to delete gatk and install t…
Comment: conda: command not found: gatk. by Pierre Lindenbaum 155k
how about all your previous questions ? take a time to validate the good answers (green mark on the left). https://www.biostars.org/p/9565…
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