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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 8.3 years ago by ★ 4.3k
32
votes
6
replies
12k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 14 months ago by 43k • written 4.0 years ago by 88k
67
votes
6
replies
26k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 15 months ago by 43k • written 11.7 years ago by 100k
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 7 weeks ago by 43k • written 6.2 years ago by 88k
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
20
votes
6
replies
5.7k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 14 months ago by 43k • written 7.7 years ago by ★ 5.2k
61
votes
6
replies
9.5k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by 43k • written 10.8 years ago by 9.7k
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 7.9 years ago by ▴ 140
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
16
votes
5
replies
9.0k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 15 months ago by 43k • written 11.7 years ago by 20k
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
29
votes
5
replies
6.4k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 14 months ago by 43k • written 10.7 years ago by ★ 4.4k
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 6.5 years ago by ▴ 800
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
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
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
6
votes
5
replies
7.0k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 12 months ago by 43k • written 6.5 years ago by ▴ 140
64
votes
5
replies
7.3k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 19 months ago by 43k • written 8.8 years ago by 12k
15
votes
5
replies
16k
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
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
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 10.5 years ago by ★ 1.2k
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
1
vote
5
replies
670
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
5
votes
5
replies
672
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 14 days ago by • 0 • written 23 days ago by ★ 3.9k
9
votes
5
replies
2.3k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 12 months ago by 43k • written 6.9 years ago by 100k
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
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 11.2 years ago by 20k
1
vote
4
replies
3.4k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 12 months ago by 43k • written 6.0 years ago by ▴ 340
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 3.3 years ago by ▴ 130
3
votes
4
replies
4.5k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 12 months ago by 43k • written 6.0 years ago by ★ 2.5k
32
votes
4
replies
8.0k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 14 months ago by 43k • written 5.5 years ago by ★ 1.6k
29
votes
4
replies
4.5k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 14 months ago by 43k • written 5.3 years ago by 27k
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 4.8 years ago by 82k
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 11.2 years ago by 11k
0
votes
4
replies
776
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
6 months ago by Coremine Medical ▴ 20
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
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 4.9 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 7.7 years ago by ★ 4.3k
10
votes
4
replies
5.7k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
9 months ago by Hamid Ghaedi 3.2k
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 8.0 years ago by ▴ 10
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 5.6 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
12
votes
4
replies
2.2k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 14 months ago by 43k • written 6.7 years ago by ▴ 590
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 9 months ago by ▴ 30 • written 7.1 years ago by ★ 1.6k
2
votes
3
replies
648
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
19
votes
3
replies
14k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 22 months ago by 43k • written 8.3 years ago by ★ 9.4k
8
votes
3
replies
2.8k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 22 months ago by 43k • written 8.3 years ago by 23k
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 5.4 years ago by 82k
11
votes
3
replies
1.4k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 13 months ago by 43k • written 7.8 years ago by 7.1k
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 13 months ago by 43k • written 7.2 years ago by ▴ 20
412 results • Page 3 of 9
Recent Votes
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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