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41
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6
replies
18k
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Tutorial: Greatly speed up conda by using mamba
software
updated 14 months ago by ▴ 40 • written 2.0 years ago by 11k
15
votes
6
replies
5.7k
views
Tutorial: How to make your snakefiles self-documenting
snakemake Tutorial
updated 6.1 years ago by ★ 2.0k • written 6.4 years ago by ★ 1.7k
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 27 days ago by 38k • written 9.2 years ago by 5.9k
11
votes
6
replies
4.5k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 8 months ago by 38k • written 7.1 years ago by ★ 4.1k
2
votes
6
replies
2.8k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
R gene Tutorial Rembrandt
updated 5.9 years ago by • 0 • written 6.7 years ago by ▴ 140
53
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 6 months ago by 38k • written 9.3 years ago by ★ 1.2k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 20 days ago by 38k • written 5.3 years ago by ▴ 740
16
votes
5
replies
8.4k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 5 weeks ago by 38k • written 10.5 years ago by 20k
5
votes
5
replies
5.9k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq Tutorial
5.4 years ago by jmzeng1314 ▴ 130
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 11 months ago by 38k • written 9.0 years ago by ★ 1.8k
20
votes
5
replies
6.1k
views
Tutorial: Analysis of single-cell RNA-seq data
RNA-Seq single-cell Tutorial
6.8 years ago by Geparada ★ 1.5k
12
votes
5
replies
7.6k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl Tutorial
6.5 years ago by Shicheng Guo ★ 9.3k
12
votes
5
replies
1.8k
views
Tutorial: FASTA file split
fasta
updated 15 days ago by 38k • written 2.8 years ago by 7.8k
10
votes
5
replies
18k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 15 days ago by 38k • written 4.7 years ago by ★ 9.3k
29
votes
5
replies
5.9k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 29 days ago by 38k • written 9.5 years ago by ★ 4.3k
9
votes
5
replies
1.9k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools Tutorial
5.7 years ago by Istvan Albert 97k
64
votes
5
replies
6.7k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 5 months ago by 38k • written 7.6 years ago by 12k
15
votes
5
replies
14k
views
Tutorial: How to create a mutation lolliplot with GenVisR
genvisr graphics bioconductor R Tutorial
updated 6.6 years ago by • 0 • written 6.8 years ago by 20k
2
votes
5
replies
1.9k
views
Tutorial: Building OMA database on SGE
oma tutorial Tutorial
updated 6.8 years ago by 127k • written 6.8 years ago by ▴ 10
6
votes
4
replies
6.9k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 4 weeks ago by 38k • written 10.0 years ago by 11k
19
votes
4
replies
8.4k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 4 weeks ago by 38k • written 10.1 years ago by 97k
3
votes
4
replies
3.3k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq Tutorial
4.4 years ago by elia.brodsky ▴ 340
32
votes
4
replies
6.4k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 12 days ago by 38k • written 4.4 years ago by ★ 1.5k
12
votes
4
replies
1.8k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 6 days ago by 38k • written 5.5 years ago by ▴ 570
12
votes
4
replies
4.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 7 weeks ago by 38k • written 2.1 years ago by ▴ 120
10
votes
4
replies
2.6k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
levlelplot correlation Tutorial
4.6 years ago by Kevin Blighe 84k
20
votes
4
replies
2.2k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 15 days ago by 38k • written 3.9 years ago by ▴ 180
15
votes
4
replies
4.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 15 days ago by 38k • written 2.7 years ago by ▴ 300
20
votes
4
replies
13k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 4 weeks ago by 38k • written 10.0 years ago by 20k
23
votes
4
replies
6.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 15 days ago by 38k • written 3.6 years ago by 70k
1
vote
4
replies
2.9k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq Tutorial
4.9 years ago by elia.brodsky ▴ 340
20
votes
4
replies
8.1k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR Tutorial
6.5 years ago by fi1d18 ★ 4.1k
34
votes
4
replies
5.5k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 4 months ago by 38k • written 7.7 years ago by ▴ 370
9
votes
4
replies
9.0k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 15 days ago by 38k • written 3.7 years ago by 4.6k
3
votes
4
replies
3.9k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus sequencing noise OpenGene Tutorial
4.9 years ago by chen ★ 2.4k
1
vote
4
replies
3.0k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs C++ compilers GNU Tutorial
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 10
28
votes
4
replies
3.7k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 14 days ago by 38k • written 4.2 years ago by 26k
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 6 weeks ago by 38k • written 11 months ago by ★ 1.7k
13
votes
3
replies
4.7k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 10 months ago by 38k • written 8.0 years ago by ▴ 860
2
votes
3
replies
1.7k
views
Tutorial: Help demonstrate reproducibility in bioinformatics with the GA4GH's tool execution Challenge
CWL Rabix GA4GH Docker Tutorial
6.1 years ago by adrian.sharma ▴ 20
6
votes
3
replies
4.1k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 14 days ago by 38k • written 4.4 years ago by ▴ 40
17
votes
3
replies
11k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 8 months ago by 38k • written 7.1 years ago by ★ 9.3k
0
votes
3
replies
2.3k
views
Tutorial: Automatic Primer Design
Assembly sequence
updated 7 months ago by 38k • written 7.4 years ago by ▴ 40
3
votes
3
replies
7.8k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
sra fastq sam Aspera Connect Tutorial
5.3 years ago by Wenhu_Cao ▴ 100
0
votes
3
replies
47k
views
Tutorial: Installation VMD on LINUX_64
VMD VMD installation gromacs Tutorial
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 10
6
votes
3
replies
5.4k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 5 weeks ago by 38k • written 10.7 years ago by 97k
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
15
votes
3
replies
4.2k
views
Tutorial: NCBI blast tutorial
ncbi blast tutorial Tutorial
updated 6.9 years ago by ▴ 540 • written 6.9 years ago by 11k
50
votes
3
replies
4.0k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 15 days ago by 38k • written 4.2 years ago by 70k
1
vote
3
replies
2.9k
views
Tutorial: resolving error of sspace_standard
Assembly software error Tutorial
6.6 years ago by reza ▴ 300
353 results • Page 3 of 8
Recent Votes
Answer: Variant caller reports a homozygous variant genotype, but more reads are associa
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
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Answer: Any tips in landing a bioinformatic job? by Vincent Laufer ★ 2.5k
Do you have a public facing github page (or equivalent) that provides examples of bioinformatics workflows you've created? For myself, if …
Comment: Align miRNA library (small RNA-seq) without trimming by Paola ▴ 10
Hi Ming Untrimmed reads have 76bp in average.
Answer: Align miRNA library (small RNA-seq) without trimming by Ming Tommy Tang ★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression by afei • 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa by rebeliscu ▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an by cfos4698 ▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking by Mensur Dlakic ★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error by Declan • 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43 by ahmad • 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43 by ahmad • 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq by dsull ★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq by dsull ★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell by lethalfang ▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set by lethalfang ▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata? by jv ★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
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