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410 results • Page 3 of 9
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30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 19 months ago by 43k • written 12.0 years ago by 100k
20
votes
6
replies
5.6k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 13 months ago by 43k • written 7.6 years ago by ★ 5.2k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 13 months ago by 43k • written 10.2 years ago by 6.0k
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 23 days 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 13 months ago by 43k • written 5.6 years ago by 16k
13
votes
6
replies
6.0k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 12 months ago by 43k • written 7.8 years ago by 14k
32
votes
6
replies
12k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 13 months ago by 43k • written 3.9 years ago by 87k
67
votes
6
replies
26k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 14 months ago by 43k • written 11.6 years ago by 100k
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
1
vote
5
replies
596
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
29
votes
5
replies
6.3k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 13 months ago by 43k • written 10.6 years ago by ★ 4.4k
12
votes
5
replies
2.4k
views
Tutorial: FASTA file split
fasta
updated 13 months ago by 43k • written 3.9 years ago by 8.5k
10
votes
5
replies
23k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 13 months ago by 43k • written 5.7 years ago by ★ 9.4k
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 7 months ago by ▴ 20 • written 8.8 years ago by ▴ 430
5
votes
5
replies
6.9k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 11 months ago by 43k • written 6.4 years ago by ▴ 130
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
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 12 months ago by 43k • written 7.9 years ago by 20k
16
votes
5
replies
13k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 13 months ago by 43k • written 6.4 years ago by ▴ 800
21
votes
5
replies
6.8k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 12 months ago by 43k • written 7.8 years ago by ★ 1.5k
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 8.7 years ago by 12k
12
votes
5
replies
8.3k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 12 months ago by 43k • written 7.9 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 18 months ago by 43k • written 10.4 years ago by ★ 1.2k
2
votes
5
replies
2.2k
views
Tutorial: Building OMA database on SGE
oma
updated 12 months ago by 43k • written 7.8 years ago by ▴ 10
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 2.0 years ago by 43k • written 10.0 years ago by ★ 1.8k
1
vote
4
replies
3.3k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 11 months ago by 43k • written 5.9 years ago by ▴ 340
24
votes
4
replies
7.6k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 13 months ago by 43k • written 4.7 years ago by 81k
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
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 6.6 years ago by ▴ 590
1
vote
4
replies
3.5k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 12 months ago by 43k • written 7.9 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 5.5 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 14 months ago by 43k • written 3.2 years ago by ▴ 130
15
votes
4
replies
4.6k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 13 months ago by 43k • written 3.7 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 11.1 years ago by 100k
20
votes
4
replies
2.6k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 13 months ago by 43k • written 4.9 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 13 months ago by 43k • written 4.8 years ago by 6.3k
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
29
votes
4
replies
4.5k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 13 months ago by 43k • written 5.2 years ago by 27k
9
votes
4
replies
5.5k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
8 months ago by Hamid Ghaedi 3.2k
0
votes
4
replies
715
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
5 months ago by Coremine Medical ▴ 20
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
8.6k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 12 months ago by 43k • written 7.6 years ago by ★ 4.3k
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
8
votes
3
replies
2.8k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 21 months ago by 43k • written 8.2 years ago by 23k
6
votes
3
replies
4.5k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 13 months ago by 43k • written 5.5 years ago by ▴ 40
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 7.0 years ago by ★ 1.6k
2
votes
3
replies
538
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
3
votes
3
replies
8.8k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 11 months ago by 43k • written 6.3 years ago by ▴ 100
51
votes
3
replies
23k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 14 months ago by 43k • written 11.3 years ago by ▴ 300
4
votes
3
replies
4.5k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 13 months ago by 43k • written 6.0 years ago by ★ 4.0k
5
votes
3
replies
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 14 months ago by 43k • written 11.4 years ago by ▴ 80
410 results • Page 3 of 9
Recent Votes
Answer: Duplicate marking, read names, and the SRA
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
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Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples by Ram 43k
Normalized how?
Comment: Duplicate marking, read names, and the SRA by GenoMax 141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa by GenoMax 141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa by Jean-Karim Heriche 27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
Comment: Duplicate marking, read names, and the SRA by Luka • 0
>Curios if there a reference for this? [Apparently it's not deprecated yet][1], but will be soon and the SRA intends for it to be at some …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
I prefer RStudio for new projects as well. The moment I need versions though, RStudio becomes a burden. I wish one could launch RStudio fro…
Comment: what's the genomic location and name of gene responsible for orange and black pa by GenoMax 141k
According to ChatGPT: The gene responsible for the orange and black patches of fur in calico cats (and tortoiseshell cats) is the X-linked …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Certainly true. Switching versions is way simpler that way, at the cost of the familiarity of the Rstudio IDE - especially if the code is w…
Comment: Duplicate marking, read names, and the SRA by GenoMax 141k
> fastq-dump is deprecated Curios if there a reference for this? `fasterq-dump` seems to allow for parallel streams but `fastq-dump` is st…
Comment: Duplicate marking, read names, and the SRA by Luka • 0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required) The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA by GenoMax 141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Done. Thank you.
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