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Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 6 days ago by 70k • written 6 days ago by ▴ 30
1
vote
0
replies
126
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
12 days ago by Milad ▴ 10
3
votes
2
replies
2.0k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
blogs Workshops conferences tutorials
updated 4 weeks ago by ▴ 970 • written 5.9 years ago by ▴ 100
5
votes
2
replies
813
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
5 weeks ago by Kevin Blighe 84k
1
vote
3
replies
1.4k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 5 weeks ago by 38k • written 11 months ago by ★ 1.7k
1
vote
0
replies
340
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
9 weeks ago by firestar ★ 1.5k
10
votes
7
replies
1.1k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 weeks ago by barslmn ★ 1.4k
1
vote
1
reply
478
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 10 weeks ago by 153k • written 10 weeks ago by ★ 1.4k
1
vote
0
replies
421
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
rRNA RNAmmer Annotation Genome
11 weeks ago by Dr.Animo ▴ 50
0
votes
0
replies
460
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo mining enrichment data Gene pathway RNA-Seq R
3 months ago by Novogene ▴ 240
1
vote
0
replies
552
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
12 weeks ago by Novogene ▴ 240
1
vote
0
replies
373
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo mining datasets data SRA RNA-Seq
3 months ago by Novogene ▴ 240
2
votes
0
replies
639
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
28 days ago by Novogene ▴ 240
44
votes
1
reply
6.2k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 6 weeks ago by 38k • written 2.5 years ago by 70k
1
vote
3
replies
421
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbs sampling splice
updated 3 months ago by 127k • written 3 months ago by ★ 1.4k
82
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 540
72
votes
60
replies
23k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 6 weeks ago by 38k • written 5.6 years ago by 84k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 6 weeks ago by 38k • written 7.1 years ago by 20k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 19 days ago by 38k • written 3.6 years ago by 7.8k
1
vote
2
replies
546
views
Tutorial: ViennaRNA package installation in Windows
install mfold viennarna rna windows
updated 6 months ago by 9.6k • written 6 months ago by ▴ 20
1
vote
0
replies
315
views
Tutorial: Making LDA Score plot
LDA metagenomics
6 months ago by rohitsatyam102 ▴ 690
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 7 days ago by ★ 1.1k • written 4.4 years ago by 84k
9
votes
7
replies
6.0k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 6 months ago by • 0 • written 2.1 years ago by ▴ 240
11
votes
1
reply
2.3k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 6 months ago by ★ 1.8k • written 14 months ago by 14k
13
votes
8
replies
3.1k
views
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
4 months ago by ATpoint 70k
82
votes
21
replies
15k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 19 days ago by 38k • written 2.5 years ago by 2.9k
27
votes
0
replies
2.7k
views
Tutorial: Building Docker images
singularity docker container
8 months ago by ATpoint 70k
1
vote
1
reply
19k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 8 months ago by ★ 2.5k • written 8 months ago by ▴ 10
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 19 days ago by 38k • written 4.8 years ago by ★ 1.3k
80
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 29 days ago by 38k • written 9.8 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 19 days ago by 38k • written 5.3 years ago by ▴ 740
37
votes
8
replies
9.3k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 19 days ago by 38k • written 2.5 years ago by 2.9k
3
votes
2
replies
1.3k
views
Tutorial: Running fastq_screen on your data
fastqscreen
12 months ago by rohitsatyam102 ▴ 690
7
votes
14
replies
2.1k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 5 months ago by • 0 • written 13 months ago by ▴ 30
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 6 weeks ago by 38k • written 9.9 years ago by 9.5k
25
votes
13
replies
6.8k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 14 months ago by ★ 1.2k • written 17 months ago by 97k
3
votes
13
replies
9.4k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 19 days ago by 38k • written 4.1 years ago by ▴ 140
13
votes
9
replies
4.1k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 9 months ago by ▴ 40 • written 16 months ago by ★ 1.1k
2
votes
0
replies
1.1k
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell Biology R Computational signalling
updated 7 weeks ago by 70k • written 15 months ago by ▴ 20
0
votes
0
replies
7.9k
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
14 months ago by Wayne ★ 1.7k
12
votes
4
replies
4.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 6 weeks ago by 38k • written 2.1 years ago by ▴ 120
26
votes
10
replies
59k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 19 days ago by 38k • written 2.0 years ago by ★ 1.3k
6
votes
2
replies
2.5k
views
Tutorial: Unsupervised clustering on gene expression data
gene RNA-seq expression clustering
6 months ago by Hamid Ghaedi 2.9k
41
votes
6
replies
18k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 14 months ago by ▴ 40 • written 2.0 years ago by 11k
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 15 days ago by 38k • written 5.3 years ago by 84k
15
votes
2
replies
1.4k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 5 months ago by ▴ 810 • written 18 months ago by ▴ 270
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 11 weeks ago by 38k • written 10.5 years ago by 20k
6
votes
2
replies
1.0k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
19 months ago by Kevin Blighe 84k
0
votes
0
replies
896
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
19 months ago by mo • 0
2
votes
0
replies
1.8k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
20 months ago by Kevin Blighe 84k
353 results • Page 1 of 8
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Answer: Samtools flagstat
Answer: Snakemake vs Nextflow Upcoming bioinformatics Project
Answer: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
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Answer: GO enrichment analysis by Antonio R. Franco ★ 5.0k
You don't mention which organism are you using. If it is a model system, you only need to select the organism, and introduce the names of …
Comment: mpileup to sync file by Pierre Lindenbaum 153k
> to a sync what is a `sync` ?
Comment: mpileup to sync file by qstefano ▴ 20
what is not clear to you?
Comment: mpileup to sync file by Pierre Lindenbaum 153k
> l to covert a mpileup file to a sync what does it mean please ?
Answer: Sites for Computer Aided Drug Designing by contact • 0
Hi, you can take a look at this [Computer-aided Enzyme Design][1] [1]: https://www.creativebiomart.net/Computer-aided-Enzyme-Design.…
Answer: installation of Snapgene tool in Ubuntu by ATpoint 70k
It's commercial software, please contact their support. In general, more than a one-liner is appreciated when asking questions.
Comment: How to demultiplex single end - dual index run - NextSeq 500 by Apex92 ▴ 260
Dear GenoMax, This is the header of my ```RunInfo.xml`` file: ``` <?xml version="1.0"?> <RunInfo xmlns:xsd="http://www.w3.org/2001/XMLSch…
Answer: Variant caller reports a homozygous variant genotype, but more reads are associa by colindaven 4.6k
You're right, but MQ=5 - so this is a really poorly mappable region. Check the QUAL field - here 6.6 - against more typical and robust …
Comment: Snakemake doesn't recognize output files even though they are created by Shred ★ 1.0k
This is the reason why the rule is executed.
Comment: Clustering with monocle 3 by fracarb8 ▴ 940
You should add some figures and the code/steps you are using. as written, your question is very subjective (e.g. how do you discriminate?),…
Answer: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran by Yuri • 0
Hi @and did you ever figure out why guppy was resulting in 90% of reads in unclassified folder? I am running into the same issue, and am…
Comment: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt by ladina.hoesli • 0
Thank you very much, this helps a lot!
Answer: Snakemake vs Nextflow Upcoming bioinformatics Project by cfos4698 ▴ 720
There are a lot of votes for Nextflow here, and it's generally pretty popular (and increasing in popularity). As a 'dissenting' voice, I'll…
Answer: Is it possible to use pseudoalignments.bam to run rMATs? by dsull ★ 4.0k
No, you can't do that with kallisto's bam files. For one, kallisto (by default) doesn't map to introns which is required by rMATs. You c…
Answer: genome annotation [sstart] [send] - how to get protein sequence from gene by shenwei356 8.0k
It means that the gene is on the negative/minus strand. So you need to compute the reverse complementary sequence before translating it to …
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