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Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 3 days ago by 70k • written 3 days ago by ▴ 20
1
vote
0
replies
119
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
9 days ago by Milad ▴ 10
3
votes
2
replies
1.9k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
blogs Workshops conferences tutorials
updated 26 days ago by ▴ 970 • written 5.9 years ago by ▴ 100
5
votes
2
replies
804
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
331
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
8 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 ★ 1.3k
1
vote
1
reply
469
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 10 weeks ago by 153k • written 10 weeks ago by ★ 1.3k
1
vote
0
replies
404
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
454
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Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo mining enrichment data Gene pathway RNA-Seq R
12 weeks ago by Novogene ▴ 240
1
vote
0
replies
548
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
365
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo mining datasets data SRA RNA-Seq
12 weeks ago by Novogene ▴ 240
2
votes
0
replies
618
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
24 days ago by Novogene ▴ 240
44
votes
1
reply
6.1k
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
417
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 ★ 1.3k
81
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 ▴ 530
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 5.5 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 7.0 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 16 days ago by 38k • written 3.6 years ago by 7.7k
1
vote
2
replies
543
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
314
views
Tutorial: Making LDA Score plot
LDA metagenomics
6 months ago by rohitsatyam102 ▴ 690
130
votes
123
replies
28k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 3 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
14k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 16 days ago by 38k • written 2.4 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
18k
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 16 days ago by 38k • written 4.8 years ago by ★ 1.3k
79
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 26 days ago by 38k • written 9.7 years ago by 11k
15
votes
5
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11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 16 days ago by 38k • written 5.3 years ago by ▴ 740
37
votes
8
replies
9.2k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 16 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 4 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 9.8 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 16 days ago by 38k • written 4.1 years ago by ▴ 140
13
votes
9
replies
4.0k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 9 months ago by ▴ 40 • written 15 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 6 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
58k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 16 days ago by 38k • written 2.0 years ago by ★ 1.3k
6
votes
2
replies
2.4k
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 11 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 10 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
895
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
1.7k
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
Recent Votes
NCBI's IgBLAST version 1.21.0 is now available
Read lengths greater than insert length
Answer: Read lengths greater than insert length
How to find promoter sequence of a gene?
Answer: How to find promoter sequence of a gene?
Comment: How to find promoter sequence of a gene?
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
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Recent Replies
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by seidel 11k
What technology is the GEO data set derived from? Signal intensity implies a fluorescence read out (i.e. microarray). If that's the case, y…
Comment: Log2 FC Threshold by seidel 11k
Given that 0.2 is a 1.15 fold change (2^0.2) you're right to be skeptical, but there's no clear answer as to the significance. Consider tha…
Comment: Read lengths greater than insert length by GenoMax 127k
As I said above the adapters are each ~60 bp long so they add ~120 bp (5' and 3' end adapters) to the length of the DNA fragment. What you …
Comment: Problem with fatsq-dump by GenoMax 127k
Looks like the developers have an answer for this error: https://github.com/ncbi/sra-tools/issues/139 At least the program seems to be ins…
Comment: Read lengths greater than insert length by shpak.max ▴ 30
I'm not claiming that all fragment lengths are exactly 50, the typical range for my data is 45-60. However, my read lengths are all 150, so…
Answer: Read lengths greater than insert length by GenoMax 127k
Illumina libraries are made by adding adapters to the ends of DNA fragment(s). Those adapters themselves are about 60 nucleotides long. Not…
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang by Rob 5.9k
If you have the raw data, you can easily get this information using [alevin-fry](https://www.nature.com/articles/s41592-022-01408-3). It pr…
Answer: Matching gene-expression data with clinical data: best practices. by pilargmarch ▴ 60
I really like using [the R/Bioconductor package TCGAbiolinks][1], it gives you clinical and expression data by patient ID. [1]: http…
Comment: Problem with fatsq-dump by Utpal • 0
with the command which fastq-dump it returns: ~/.conda/envs/sratoolkit_env/bin/fastq-dump With fastq-dump I get the following error …
Comment: Calculation method of RMSMappingQuality by zhangfish ▴ 40
Maybe, I think the formal (1) is correct for most situations (for example the earlier version of GATK). However, there are some changes in …
Comment: error in downloading of some accesions with fastq-dump by Utpal • 0
Hi, could you please let me know how to upgrade sratoolkit in centos? Thanks and regards,
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang by benformatics 3.5k
I don't think you can get that information specifically: https://kb.10xgenomics.com/hc/en-us/articles/360021902671-Can-we-detect-splice-va…
Comment: Remove part of headers in FASTA file by Pierre Lindenbaum 153k
Use `cut -d ' '`
Comment: Problem running interproscan-5.15-54.0 for protein sequences by Pratyay • 0
Hi, can you guide me how to compile the src folder? Many thanks!
Comment: Matching gene-expression data with clinical data: best practices. by krushnach80 ★ 1.1k
You can check [this][1] [1]: https://www.linkedomics.org/
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