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47
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19
replies
12k
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8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 11 weeks ago by 38k • written 10.1 years ago by 97k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 15 days ago by 38k • written 2.7 years ago by ▴ 690
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
44
votes
1
reply
6.2k
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
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational biology Tutorial
7.0 years ago by Sinji ★ 3.2k
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
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
15 days ago by Ram 38k
42
votes
19
replies
7.1k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 4 weeks ago by 38k • written 10.1 years ago by 4.1k
42
votes
16
replies
21k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 7 months ago by 38k • written 7.5 years ago by ★ 2.3k
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
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 23 days ago by 38k • written 9.0 years ago by ★ 1.9k
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
chromosome karyotype R ggplot2 Tutorial
updated 5.4 years ago by ★ 3.4k • written 5.6 years ago by ★ 3.3k
37
votes
8
replies
9.3k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 20 days ago by 38k • written 2.5 years ago by 2.9k
34
votes
15
replies
5.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 15 days ago by 38k • written 3.8 years ago by ★ 9.3k
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
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 14 days ago by 38k • written 6.5 years ago by ▴ 310
33
votes
16
replies
15k
views
10 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 28 days ago by 38k • written 9.4 years ago by 20k
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
31
votes
6
replies
8.7k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 15 days ago by 38k • written 2.9 years ago by 84k
31
votes
9
replies
24k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 15 days ago by 38k • written 2.6 years ago by ▴ 140
31
votes
12
replies
26k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 29 days ago by 38k • written 9.5 years ago by 97k
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 6 months ago by 38k • written 10.9 years ago by 97k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 23 days ago by 38k • written 9.0 years ago by ▴ 800
30
votes
14
replies
15k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 4 weeks ago by 38k • written 10.2 years ago by 5.9k
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
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
27
votes
0
replies
2.7k
views
Tutorial: Building Docker images
singularity docker container
8 months ago by ATpoint 70k
26
votes
10
replies
59k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 20 days ago by 38k • written 2.0 years ago by ★ 1.3k
26
votes
17
replies
6.7k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 6 months ago by 38k • written 8.6 years ago by 5.9k
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 15 days ago by 38k • written 3.5 years ago by 19k
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
24
votes
15
replies
7.9k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 4 weeks ago by 38k • written 10.2 years ago by 9.5k
23
votes
19
replies
5.7k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
mutation fastq cancer target Tutorial
updated 5.2 years ago by • 0 • written 6.5 years ago by ★ 2.4k
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
23
votes
8
replies
4.9k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 15 months ago by 38k • written 8.6 years ago by 24k
22
votes
1
reply
3.0k
views
Tutorial: Introduction To R Course Materials Available
R
updated 12 weeks ago by 38k • written 10.9 years ago by 26k
22
votes
2
replies
5.5k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
pipeline workflow management Tutorial
updated 4.5 years ago by ▴ 160 • written 6.4 years ago by ★ 2.0k
21
votes
2
replies
3.7k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 6 months ago by ▴ 40 • written 23 months ago by 7.8k
20
votes
14
replies
3.2k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization EaSeq Tutorial Windows
6.9 years ago by Mads Lerdrup ▴ 460
20
votes
2
replies
6.9k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome Tutorial
written 5.4 years ago by ★ 3.4k
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
20
votes
10
replies
4.7k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 15 days ago by 38k • written 2.6 years ago by 11k
20
votes
0
replies
8.4k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
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
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
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
20
votes
7
replies
5.6k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 15 days ago by 38k • written 4.5 years ago by ▴ 740
20
votes
6
replies
4.8k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 15 days ago by 38k • written 6.5 years ago by ★ 5.2k
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
353 results • Page 2 of 8
Recent Votes
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?
Answer: Somatic truth set
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Recent Replies
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…
Comment: GO enrichment analysis by Jeremy ▴ 780
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job? by Carambakaracho ★ 3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
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