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356 results • Page 3 of 8
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10
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1
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7.7k
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Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 16 days ago by 39k • written 5.7 years ago by ▴ 110
12
votes
5
replies
7.7k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 8 weeks ago by 39k • written 7.0 years ago by ★ 9.3k
0
votes
0
replies
7.6k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 14 days ago by 39k • written 5.4 years ago by ▴ 10
6
votes
1
reply
7.6k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 3 months ago by 39k • written 11.0 years ago by 98k
16
votes
11
replies
7.5k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
11 weeks ago by Ram 39k
18
votes
22
replies
7.4k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 11 weeks ago by 39k • written 3.5 years ago by 7.9k
11
votes
2
replies
7.4k
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 21 days ago by 39k • written 6.2 years ago by ★ 1.5k
12
votes
0
replies
7.4k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 13 months ago by 39k • written 8.3 years ago by ★ 4.6k
45
votes
28
replies
7.3k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
14 days ago by Ram 39k
11
votes
7
replies
7.2k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 13 days ago by 39k • written 2.2 years ago by ▴ 300
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
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 15 days ago by 39k • written 5.5 years ago by ★ 3.4k
6
votes
4
replies
7.0k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 3 months ago by 39k • written 10.2 years ago by 11k
60
votes
2
replies
7.0k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
4
votes
2
replies
6.9k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 3 months ago by 39k • written 11.0 years ago by 98k
64
votes
5
replies
6.8k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 7 months ago by 39k • written 7.8 years ago by 12k
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
12
votes
11
replies
6.7k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 22 days ago by 39k • written 6.2 years ago by ★ 2.4k
32
votes
4
replies
6.6k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 10 weeks ago by 39k • written 4.6 years ago by ★ 1.5k
49
votes
1
reply
6.6k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 3 months ago by 39k • written 2.7 years ago by 72k
15
votes
2
replies
6.5k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 3 months ago by 39k • written 10.8 years ago by 98k
2
votes
0
replies
6.5k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 14 days ago by 39k • written 5.5 years ago by ▴ 310
23
votes
4
replies
6.4k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 11 weeks ago by 39k • written 3.8 years ago by 72k
15
votes
1
reply
6.4k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 15 days ago by 39k • written 5.5 years ago by ★ 3.0k
15
votes
0
replies
6.4k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 3 months ago by 39k • written 10.9 years ago by 98k
8
votes
2
replies
6.3k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 16 months ago by 39k • written 8.6 years ago by 12k
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
8
votes
12
replies
6.2k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 8 weeks ago by 39k • written 7.0 years ago by 13k
14
votes
2
replies
6.2k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 9 weeks ago by 39k • written 7.7 years ago by ★ 2.9k
5
votes
5
replies
6.1k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 15 days ago by 39k • written 5.6 years ago by ▴ 130
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
6
votes
0
replies
6.0k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 3 months ago by 39k • written 11.1 years ago by ▴ 360
29
votes
5
replies
5.9k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 3 months ago by 39k • written 9.7 years ago by ★ 4.3k
4
votes
1
reply
5.9k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 3 months ago by 39k • written 11.1 years ago by ▴ 360
16
votes
6
replies
5.8k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 7 weeks ago by 39k • written 6.6 years ago by ★ 1.7k
23
votes
19
replies
5.8k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 7 weeks ago by 39k • written 6.7 years ago by ★ 2.4k
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 11 weeks ago by 39k • written 4.6 years ago by ▴ 750
14
votes
7
replies
5.6k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 11 weeks ago by 39k • written 7.0 years ago by ★ 3.3k
22
votes
2
replies
5.6k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 7 weeks ago by 39k • written 6.6 years ago by ★ 2.1k
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
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 20 days ago by 39k • written 6.1 years ago by 5.2k
6
votes
3
replies
5.4k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 3 months ago by 39k • written 10.9 years ago by 98k
34
votes
15
replies
5.3k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 11 weeks ago by 39k • written 4.0 years ago by ★ 9.3k
13
votes
6
replies
5.3k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 8 weeks ago by 39k • written 7.0 years ago by 14k
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 11 weeks ago by 39k • written 2.7 years ago by 12k
9
votes
2
replies
5.2k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 140
7
votes
0
replies
5.1k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 3 months ago by 39k • written 11.0 years ago by ▴ 120
12
votes
31
replies
5.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 12 weeks ago by 39k • written 3.8 years ago by 7.9k
0
votes
2
replies
5.1k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 19 months ago by 39k • written 8.9 years ago by 9.6k
3
votes
2
replies
5.0k
views
Tutorial: Reorder Vcf Files
vcf
updated 3 months ago by 39k • written 10.1 years ago by ▴ 60
356 results • Page 3 of 8
Recent Votes
Answer: How to extract haplotype data from phased bcf files
Answer: How to extract haplotype data from phased bcf files
Comment: My kernel is killing the pairtools dedup script, how to prevent that?
Comment: ggsave() bug in ggplot2?
Comment: BioInformatics, Software
Comment: Single Cell Rna Seq Using BD Rhapsody
Comment: DP meaning in VCF files
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Comment: How to extract haplotype data from phased bcf files by Lynne-95 • 0
Thanks that worked perfectly!
Answer: How to extract haplotype data from phased bcf files by Pierre Lindenbaum 154k
use %TGT (translated genotype) $ bcftools query -f '[%CHROM %POS %TGT\n]'
Comment: convert data frame with character column to data frame with integer column by Basti ★ 1.5k
You would better give an example with values because we don't know what is in each variable so we cannot give you a precise code, but seems…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by ATpoint 72k
This information is annotated in GTF files. You can get them for almost every annotated species from Ensembl. There is a column `gene_bioty…
Answer: DE genes across multiple scRNAseq clusters-are they significantly enriched? by ATpoint 72k
First of all, with thousands of DEGs you might want to choose a DE framework that allows testing against a fold change threshold, such as `…
Comment: PacBio Pipeline and Tools for Variant Call by Kiran ▴ 80
Thanks a lot William, I am Clear now
Comment: The famous WGS dataset, Ashkenazi Trio? by cmdcolin ★ 3.0k
what is valuable information to you
Answer: Why weblogo of biopython doesn't work? by minakshiboruahassam • 0
The weblogo3 application is giving same file even if u run the scripts separately on python standalone or whatever. The weblogo command is …
Answer: Make a BedGraph file by rfran010 ▴ 80
I would suggest bedtools makewindows to generate your 3,000bp bins then bedtools coverage to generate fraction of repeats over your windows…
Answer: What is the best way to clean bulk RNA-seq data? by rfran010 ▴ 80
Honestly, I am a fan of visualizing to select a threshold since these can depend on the specific experiment. I would even just run standard…
Answer: Help with running ATAC using Encode pipeline by rfran010 ▴ 80
Read all instructions carefully Specifically, this info is under the "Input JSON file specification" section with details in the followin…
Answer: BioInformatics, Software by rfran010 ▴ 80
There have been some good suggestions, but it seems like you may be asking one of two questions, either (1) how to do bioinformatics? or (2…
Answer: Genome assembly statistical tools by Bryan • 0
I'll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I'll then polish my…
Comment: how to design a guide RNA by rfran010 ▴ 80
I agree this is very basic CRISPR mechanism and you'd be better off reading sites that could explain better than me. However, there is a lo…
Comment: ATAC peak-calling: same peak ID across multiple experimental conditions? by rfran010 ▴ 80
You want to use the MACS2 score columns? You can retain these with bedtools option `-c` . This will retain the score columns from any merge…
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