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48
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 4 months ago by 39k • written 10.3 years ago by 98k
45
votes
28
replies
7.4k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
20 days ago by Ram 39k
45
votes
14
replies
66k
views
10 follow
Tutorial: Using R in Conda
R
updated 12 weeks ago by 39k • written 2.9 years ago by ▴ 690
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 3 months ago by 39k • written 11.2 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
updated 9 weeks ago by 39k • written 7.2 years ago by ★ 3.2k
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 3 months ago by 39k • written 9.4 years ago by 5.9k
42
votes
19
replies
7.2k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 3 months ago by 39k • written 10.3 years ago by 4.1k
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
42
votes
6
replies
19k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 16 months ago by ▴ 40 • written 2.2 years ago by 12k
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 10 months ago by 39k • written 7.7 years ago by ★ 2.3k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 3 months ago by 39k • written 9.2 years ago by ★ 1.9k
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 22 days ago by 39k • written 5.8 years ago by ★ 3.3k
38
votes
8
replies
10k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 3 months ago by 39k • written 2.7 years ago by 2.9k
34
votes
4
replies
5.6k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 6 months ago by 39k • written 7.9 years ago by ▴ 370
34
votes
15
replies
5.4k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 12 weeks ago by 39k • written 4.0 years ago by ★ 9.3k
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 12 weeks ago by 39k • written 6.7 years ago by ▴ 310
34
votes
17
replies
15k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 4 weeks ago by 130k • written 9.5 years ago by 20k
32
votes
4
replies
6.6k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 11 weeks ago by 39k • written 4.6 years ago by ★ 1.5k
31
votes
12
replies
27k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 3 months ago by 39k • written 9.6 years ago by 98k
31
votes
9
replies
27k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 12 weeks ago by 39k • written 2.8 years ago by ▴ 140
31
votes
6
replies
9.5k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 12 weeks ago by 39k • written 3.0 years ago by 85k
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 8 months ago by 39k • written 11.1 years ago by 98k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 3 months ago by 39k • written 9.2 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 3 months ago by 39k • written 10.3 years ago by 5.9k
29
votes
5
replies
6.0k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 3 months ago by 39k • written 9.7 years ago by ★ 4.3k
28
votes
4
replies
3.9k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 12 weeks ago by 39k • written 4.4 years ago by 26k
27
votes
0
replies
2.9k
views
Tutorial: Building Docker images
singularity docker container
10 months ago by ATpoint 72k
27
votes
13
replies
8.3k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 16 months ago by ★ 1.2k • written 20 months ago by 98k
26
votes
10
replies
63k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 3 months ago by 39k • written 2.2 years ago by ★ 1.3k
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 12 weeks ago by 39k • written 3.6 years ago by 19k
26
votes
17
replies
6.8k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 8 months ago by 39k • written 8.8 years ago by 5.9k
24
votes
15
replies
8.1k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 3 months ago by 39k • written 10.4 years ago by 9.6k
23
votes
19
replies
5.8k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 2.4k
23
votes
4
replies
6.4k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 12 weeks ago by 39k • written 3.8 years ago by 72k
23
votes
8
replies
5.0k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 17 months ago by 39k • written 8.8 years ago by 24k
22
votes
1
reply
3.0k
views
Tutorial: Introduction To R Course Materials Available
R
updated 5 months ago by 39k • written 11.1 years ago by 26k
22
votes
2
replies
5.6k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 8 weeks ago by 39k • written 6.6 years ago by ★ 2.1k
21
votes
10
replies
5.2k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 12 weeks ago by 39k • written 2.8 years ago by 12k
21
votes
2
replies
4.1k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 9 months ago by ▴ 40 • written 2.1 years ago by 7.9k
20
votes
6
replies
5.0k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 12 weeks ago by 39k • written 6.7 years ago by ★ 5.2k
20
votes
7
replies
5.7k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 12 weeks ago by 39k • written 4.6 years ago by ▴ 750
20
votes
4
replies
8.2k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 4.2k
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 21 days ago by 39k • written 5.5 years ago by ★ 3.4k
20
votes
4
replies
2.3k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 12 weeks ago by 39k • written 4.1 years ago by ▴ 180
20
votes
0
replies
8.4k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
20
votes
4
replies
13k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 3 months ago by 39k • written 10.2 years ago by 20k
20
votes
5
replies
6.3k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 8 weeks ago by 39k • written 6.9 years ago by ★ 1.5k
20
votes
14
replies
3.4k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 8 weeks ago by 39k • written 7.1 years ago by ▴ 460
19
votes
9
replies
6.1k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
358 results • Page 2 of 8
Recent Votes
NM_transcript ID gene identification
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
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Recent Replies
Comment: pal2nal -nogap -nomismatch options not working by Marie • 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq? by camillab. ▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq? by camillab. ▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq? by rpolicastro 12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq? by Trivas ★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap? by Ram 39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag by Ram 39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database by PeterC_NCBI ▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R by rohitsatyam102 ▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38 by GenoMax 130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag by Pierre Lindenbaum 154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b by Ram 39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag by Ram 39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38 by heureuse • 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b by Arup Ghosh 3.2k
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