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Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 22 months ago by 43k • written 8.2 years ago by ★ 4.3k
13
votes
6
replies
6.0k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 13 months ago by 43k • written 7.9 years ago by 14k
2
votes
6
replies
3.2k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 13 months ago by 43k • written 7.8 years ago by ▴ 140
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 6 weeks ago by 43k • written 6.2 years ago by 87k
106
votes
6
replies
26k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 14 months ago by 43k • written 5.7 years ago by 16k
67
votes
6
replies
26k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 14 months ago by 43k • written 11.7 years ago by 100k
61
votes
6
replies
9.5k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by 43k • written 10.7 years ago by 9.7k
20
votes
6
replies
5.6k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 14 months ago by 43k • written 7.6 years ago by ★ 5.2k
5
votes
5
replies
606
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 4 days ago by • 0 • written 13 days ago by ★ 3.9k
16
votes
5
replies
9.0k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 14 months ago by 43k • written 11.6 years ago by 20k
10
votes
5
replies
24k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 14 months ago by 43k • written 5.8 years ago by ★ 9.4k
29
votes
5
replies
6.4k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 14 months ago by 43k • written 10.6 years ago by ★ 4.4k
2
votes
5
replies
2.2k
views
Tutorial: Building OMA database on SGE
oma
updated 13 months ago by 43k • written 7.9 years ago by ▴ 10
12
votes
5
replies
2.5k
views
Tutorial: FASTA file split
fasta
updated 14 months ago by 43k • written 3.9 years ago by 8.6k
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 2.1 years ago by 43k • written 10.1 years ago by ★ 1.8k
1
vote
5
replies
637
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
12
votes
5
replies
8.4k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 13 months ago by 43k • written 8.0 years ago by ★ 9.4k
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 13 months ago by 43k • written 7.9 years ago by 20k
64
votes
5
replies
7.3k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 18 months ago by 43k • written 8.8 years ago by 12k
5
votes
5
replies
7.0k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 11 months ago by 43k • written 6.5 years ago by ▴ 130
54
votes
5
replies
15k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 19 months ago by 43k • written 10.4 years ago by ★ 1.2k
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 8 months ago by ▴ 20 • written 8.8 years ago by ▴ 430
21
votes
5
replies
6.8k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 13 months ago by 43k • written 7.9 years ago by ★ 1.5k
9
votes
5
replies
2.3k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by 43k • written 6.8 years ago by 100k
16
votes
5
replies
13k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 14 months ago by 43k • written 6.4 years ago by ▴ 800
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 14 months ago by 43k • written 11.1 years ago by 20k
10
votes
4
replies
5.6k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
9 months ago by Hamid Ghaedi 3.2k
6
votes
4
replies
7.5k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 14 months ago by 43k • written 11.1 years ago by 11k
20
votes
4
replies
2.7k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 14 months ago by 43k • written 5.0 years ago by ▴ 180
32
votes
4
replies
7.9k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 13 months ago by 43k • written 5.5 years ago by ★ 1.6k
3
votes
4
replies
4.5k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 11 months ago by 43k • written 6.0 years ago by ★ 2.5k
3
votes
4
replies
3.6k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 11 months ago by 43k • written 5.5 years ago by ▴ 340
24
votes
4
replies
7.7k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 14 months ago by 43k • written 4.7 years ago by 82k
10
votes
4
replies
11k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 14 months ago by 43k • written 4.8 years ago by 6.4k
20
votes
4
replies
8.6k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 13 months ago by 43k • written 7.6 years ago by ★ 4.3k
12
votes
4
replies
2.2k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 13 months ago by 43k • written 6.7 years ago by ▴ 590
12
votes
4
replies
5.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 15 months ago by 43k • written 3.2 years ago by ▴ 130
29
votes
4
replies
4.5k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 13 months ago by 43k • written 5.3 years ago by 27k
0
votes
4
replies
748
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
5 months ago by Coremine Medical ▴ 20
15
votes
4
replies
4.6k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 14 months ago by 43k • written 3.8 years ago by ▴ 340
1
vote
4
replies
3.4k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 11 months ago by 43k • written 6.0 years ago by ▴ 340
19
votes
4
replies
8.9k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 14 months ago by 43k • written 11.2 years ago by 100k
1
vote
4
replies
3.5k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 13 months ago by 43k • written 7.9 years ago by ▴ 10
8
votes
3
replies
2.8k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 22 months ago by 43k • written 8.2 years ago by 23k
2
votes
3
replies
2.0k
views
Tutorial: Help demonstrate reproducibility in bioinformatics with the GA4GH's tool execution Challenge
GA4GH Docker CWL Rabix
updated 12 months ago by 43k • written 7.2 years ago by ▴ 20
3
votes
3
replies
1.2k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 4 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
14
votes
3
replies
20k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 8 months ago by ▴ 30 • written 7.1 years ago by ★ 1.6k
5
votes
3
replies
5.4k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 13 months ago by • 0 • written 6.5 years ago by ▴ 130
50
votes
3
replies
4.8k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 14 months ago by 43k • written 5.3 years ago by 82k
4
votes
3
replies
4.6k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 14 months ago by 43k • written 6.1 years ago by ★ 4.0k
412 results • Page 3 of 9
Recent Votes
Answer: Is therer any suggestions on mapping rate of WGBS data?
A: Download full list of SNPs and their coordinates in hg38
Answer: HCL database download
Answer: Tissue-specific DEG analysis with DEseq2
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: How to access TCGA samples that were treated with a specific drug?
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Popular Question to Tastulek • 0
Scholar to sooni ▴ 20
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Comment: Is therer any suggestions on mapping rate of WGBS data? by Zeng Jingyu ▴ 60
Thank you for your answer!
Answer: HCL database download by sooni ▴ 20
I solved the problem by conneting another internet exploer. I think it was probably a problem with Chrome itself.
Answer: barcode of TCR-sequencing by mizraelson ▴ 60
Hi, What protocol did you use for TCR-seq library preparation? Generally speaking, there is no need to remove barcodes, as MiXCR can work …
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C by qwertyuiop26 • 0
I've implemented fm index with backward search and need an inexact search to implement on FM index, I couldn't understand how fm index coul…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative by Qroid ▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v by sainavyav22 • 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases by jared.andrews07 ★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype by GenoMax 142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
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