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353 results • Page 2 of 8
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47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 20 days ago by 37k • written 9.9 years ago by 96k
45
votes
14
replies
52k
views
10 follow
Tutorial: Using R in Conda
R Tutorial
updated 3 months ago by ▴ 20 • written 2.5 years ago by ▴ 690
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa tutorial Tutorial
updated 18 months ago by • 0 • written 10.8 years ago by ▴ 540
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
6.8 years ago by Sinji ★ 3.2k
42
votes
33
replies
6.6k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
2.2 years ago by Ram 37k
42
votes
19
replies
7.0k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software tutorial Tutorial
9.9 years ago by Daniel Standage 4.1k
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
Tutorial papers sequencing
updated 16 months ago by 37k • written 10.4 years ago by 96k
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 5 months ago by 37k • written 7.4 years ago by ★ 2.3k
41
votes
1
reply
5.8k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger tutorial rna-seq
6 weeks ago by ATpoint 68k
41
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf vcf ensembl tcga somatic Tutorial
2.1 years ago by Cyriac Kandoth 5.8k
41
votes
6
replies
16k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 12 months ago by ▴ 40 • written 22 months ago by 10k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell Tutorial flow-cytometry
9 weeks ago by Ahill ★ 1.9k
39
votes
6
replies
16k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
chromosome karyotype R ggplot2 Tutorial
updated 5.2 years ago by ★ 3.4k • written 5.4 years ago by ★ 3.3k
37
votes
8
replies
8.6k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer Tutorial R methylation
updated 8 weeks ago by ★ 1.1k • written 2.3 years ago by 2.8k
34
votes
15
replies
4.7k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf Tutorial
updated 11 months ago by 37k • written 3.6 years ago by ★ 9.2k
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
R TCGA GDC next-gen Tutorial
updated 3.9 years ago by ▴ 30 • written 6.3 years ago by ▴ 310
34
votes
4
replies
5.5k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 11 weeks ago by 37k • written 7.5 years ago by ▴ 370
33
votes
16
replies
14k
views
10 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
classification tutorial Tutorial
5.8 years ago by Obi Griffith 20k
32
votes
4
replies
6.2k
views
Tutorial: Fast LD computation from VCF files using tomahawk
vcf vcftools bcftools ld snp Tutorial
4.2 years ago by firestar ★ 1.5k
31
votes
6
replies
8.0k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
17 months ago by Kevin Blighe 84k
31
votes
9
replies
22k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 8 months ago by • 0 • written 2.5 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
Tutorial qualitycontrol fastqc tutorial
updated 14 months ago by 37k • written 9.3 years ago by 96k
30
votes
14
replies
14k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
install genome music linux smg Tutorial
6.3 years ago by Cyriac Kandoth 5.8k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
bioinformatics pipeline python tutorial Tutorial
updated 8 months ago by 37k • written 8.8 years ago by ▴ 800
29
votes
5
replies
5.8k
views
Tutorial: Gnu Parallel Tutorial
parallel tools tutorial tutorial Tutorial
9.4 years ago by ole.tange ★ 4.3k
29
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 4 months ago by 37k • written 10.8 years ago by 96k
28
votes
4
replies
3.5k
views
Tutorial: Modern Statistics for Modern Biology
statistics Tutorial
4.0 years ago by Jean-Karim Heriche 26k
27
votes
0
replies
2.5k
views
Tutorial: Building Docker images
singularity docker container
6 months ago by ATpoint 68k
26
votes
0
replies
2.0k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
variant interpretation annotation clinical cancer Tutorial
2.3 years ago by Malachi Griffith 19k
26
votes
17
replies
6.5k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 4 months ago by 37k • written 8.5 years ago by 5.9k
24
votes
13
replies
5.7k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 12 months ago by ★ 1.1k • written 15 months ago by 96k
24
votes
10
replies
55k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
Tutorial error software R
updated 8 months ago by • 0 • written 22 months ago by ★ 1.3k
24
votes
15
replies
7.8k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
bioinformatics training tutorial Tutorial
10 months ago by Medhat 9.5k
23
votes
8
replies
4.8k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 13 months ago by 37k • written 8.4 years ago by 24k
23
votes
4
replies
6.0k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap chip-seq atac-seq heatmap Tutorial
updated 19 months ago by ★ 1.2k • written 3.5 years ago by 68k
23
votes
19
replies
5.5k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
mutation fastq cancer target Tutorial
updated 5.0 years ago by • 0 • written 6.3 years ago by ★ 2.4k
22
votes
2
replies
5.5k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
pipeline workflow management Tutorial
updated 4.3 years ago by ▴ 160 • written 6.3 years ago by ★ 2.0k
22
votes
1
reply
2.9k
views
Tutorial: Introduction To R Course Materials Available
R
updated 27 days ago by 37k • written 10.8 years ago by 26k
21
votes
2
replies
3.3k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 4 months ago by ▴ 40 • written 21 months ago by 7.5k
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
6.7 years ago by Mads Lerdrup ▴ 460
20
votes
7
replies
5.5k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
RNA-Seq R ggplot2 Tutorial
2.8 years ago by ahmad mousavi ▴ 740
20
votes
5
replies
6.0k
views
Tutorial: Analysis of single-cell RNA-seq data
RNA-Seq single-cell Tutorial
6.6 years ago by Geparada ★ 1.5k
20
votes
4
replies
2.1k
views
Tutorial: Bash One-liners collection on Github
bash-oneliners linux shell bioinformatics bash Tutorial
written 3.7 years ago by ▴ 180
20
votes
2
replies
6.8k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome Tutorial
written 5.2 years ago by ★ 3.4k
20
votes
4
replies
13k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix tutorial Tutorial
updated 4.5 years ago by ▴ 10 • written 9.9 years ago by 20k
20
votes
4
replies
8.1k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR Tutorial
6.4 years ago by fi1d18 ★ 4.1k
20
votes
6
replies
4.7k
views
Tutorial: Open Targets and programmatic access
drug API bioinformatics open targets disease Tutorial
2.6 years ago by Denise CS ★ 5.2k
19
votes
2
replies
3.0k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS for beginners Tutorial
updated 5.8 years ago by ▴ 10 • written 5.8 years ago by ▴ 640
19
votes
0
replies
8.3k
views
Tutorial: Metagenomics Review Papers
papers metagenomics tutorial Tutorial
10.0 years ago by Istvan Albert 96k
19
votes
4
replies
8.3k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
rna-seq tutorial Tutorial
6.1 years ago by Istvan Albert 96k
353 results • Page 2 of 8
Recent Votes
Answer: Looking for a tool which provides mapping quality score distributions from BAM f
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: Gviz python alternative
Answer: Gviz python alternative
Answer: Annotating snps with gene information
Comment: Plotting Correlation matrix
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Recent Replies
Answer: Python Dictionary of Primer3-py Primer Designs by barslmn ★ 1.2k
You're so close. You can simply loop over sequence dictionaries like you did with the `design_output` and check if the keys with `startswit…
Comment: Unable to install clusterProfiler on Mac M1 by GenoMax 125k
Have you installed `Xcode` and the command line tools that go with? If not you will need to install those.
Answer: SRA taxonomy analysis by Steve • 0
Thanks @genomax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/ I wonder if it …
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives? by demoraesdiogo2017 ▴ 80
thanks! however, shouldn't it also have a gtf/gff file with the annotations?
Comment: Getting a VCF file from plink .bed, .fam and .bim files by hi.there • 0
Thanks Ram. Yes. I have read all of this documentation before. --file and --bfile. I have actually tried doing the complete liftover be…
Answer: SRA taxonomy analysis by GenoMax 125k
This data may only be available using `BigQuery` for [**SRA in cloud**][1]. For more information on querying: https://www.ncbi.nlm.nih.g…
Comment: MesKit error message - Join columns must be present in data. by CH1374 • 0
column names for the maf are: [1] "Hugo_Symbol" "Chromosome" "Start_Position" [4] "End_Position" "Variant_Classification" "Variant_Type" [7…
Answer: scaffold assembly inro chromosomal assembly using reference genome by samuel.a.odonnell ▴ 450
Have a look at ragtag and ragout. I use ragout for smaller assemblies (~20 Mb and less) and ragtag for larger genomes.
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl by Ram 37k
I've been meaning to work on a Biostars-specific code formatting manual for a while now but the basic is pretty simple: You can use backtic…
Comment: Multiline Fasta To Single Line Fasta by Onur • 0
Thank you it's also worked for me too. Best,
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl by Estefania ▴ 10
Thanks Ram. Could you point to a manual on how to make the post look like yours? I just copy-pasted my R script and this is how it shows in…
Comment: extracting input files form Seurat by rasing02 • 0
Thank you jared.andrews07
Comment: extracting input files form Seurat by rasing02 • 0
Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature p…
Comment: Downloading 450k methylation data from GEO by GenoMax 125k
I don't think they have provided processed data as a single upload.
Answer: extracting input files form Seurat by jared.andrews07 ★ 14k
You can get the data behind any of the plots easily enough: ``` p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by…
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