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111
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Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
1 day ago by Coremine Medical ▴ 10
1
vote
0
replies
120
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 2 days ago by 39k • written 2 days ago by ▴ 10
3
votes
0
replies
332
views
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 130k • written 9.5 years ago by 20k
2
votes
0
replies
465
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 11 weeks ago by 72k • written 11 weeks ago by ▴ 40
1
vote
0
replies
288
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 26 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
476
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
9 weeks ago by barslmn ★ 1.6k
1
vote
1
reply
789
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
731
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
622
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
746
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
564
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
518
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 3 months ago by 39k • written 3.8 years ago by 7.9k
1
vote
2
replies
755
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
406
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 19 days ago by 39k • written 2.3 years ago by ▴ 300
12
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
4.3k
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 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 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 11 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 10.1 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 12 weeks 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 7 days ago by 39k • written 17 months ago by ▴ 20
0
votes
0
replies
9.4k
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
358 results • Page 1 of 8
Recent Votes
Answer: Saving results from yeastgenome.org blastp search
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
Answer: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
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Popular Question to Payal ▴ 140
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Recent Replies
Comment: VCF file CSQ flag by Payal ▴ 140
Its a gvcf file #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S101 S102 S103 S104 S105
Comment: CellRanger problem by GenoMax 130k
And how much memory do you have assigned for this job? Likely you do not have enough memory for this process.
Comment: VCF file CSQ flag by Ram 39k
> a g.VCF file A `.vcf` file or a `gvcf` file?
Comment: CellRanger problem by Ram 39k
What is the cellranger command you're using?
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by Yeeshouw • 0
I see, I believe I was running an older version or have missed the option, I have updated to v2.10.5 and can see this option now. Thank you…
Answer: Saving results from yeastgenome.org blastp search by GenoMax 130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38 by GenoMax 130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions by B.N. • 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions by B.N. • 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq by GenoMax 130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions by Sasha ▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq by solarchan7 • 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome by Basti ★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions by ATpoint 72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
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