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409 results • Page 3 of 9
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20
votes
0
replies
8.7k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 14 months ago by 43k • written 11.6 years ago by 100k
9
votes
0
replies
8.7k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 14 months ago by 43k • written 12.0 years ago by ▴ 540
49
votes
1
reply
8.7k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 14 months ago by 43k • written 3.6 years ago by 81k
20
votes
4
replies
8.6k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 12 months ago by 43k • written 7.6 years ago by ★ 4.3k
81
votes
8
replies
8.5k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 13 months ago by 43k • written 9.9 years ago by 19k
12
votes
5
replies
8.3k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 12 months ago by 43k • written 7.9 years ago by ★ 9.4k
14
votes
0
replies
8.3k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 860
8
votes
7
replies
8.3k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 2.2 years ago by 43k • written 10.4 years ago by ★ 2.6k
16
votes
11
replies
8.2k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
13 months ago by Ram 43k
0
votes
0
replies
8.1k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
20
votes
2
replies
8.1k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 11 months ago by 43k • written 6.4 years ago by ★ 3.4k
32
votes
4
replies
7.9k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 13 months ago by 43k • written 5.5 years ago by ★ 1.6k
12
votes
0
replies
7.8k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 2.0 years ago by 43k • written 9.2 years ago by ★ 4.7k
42
votes
19
replies
7.8k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 14 months ago by 43k • written 11.1 years ago by 4.1k
6
votes
1
reply
7.8k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 14 months ago by 43k • written 11.9 years ago by 100k
26
votes
17
replies
7.7k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 19 months ago by 43k • written 9.7 years ago by 6.0k
24
votes
4
replies
7.6k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 13 months ago by 43k • written 4.7 years ago by 81k
12
votes
11
replies
7.5k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 11 months ago by 43k • written 7.1 years ago by ★ 2.4k
6
votes
4
replies
7.5k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 14 months ago by 43k • written 11.1 years ago by 11k
60
votes
2
replies
7.4k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 14 months ago by 43k • written 11.6 years ago by 100k
64
votes
5
replies
7.3k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 18 months ago by 43k • written 8.7 years ago by 12k
4
votes
2
replies
7.2k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 14 months ago by 43k • written 11.9 years ago by 100k
15
votes
1
reply
7.1k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 11 months ago by 43k • written 6.4 years ago by ★ 3.0k
16
votes
9
replies
7.0k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 22 months ago by ▴ 70 • written 2.4 years ago by ★ 1.3k
22
votes
10
replies
7.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 13 months ago by 43k • written 3.6 years ago by 13k
5
votes
5
replies
6.9k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 11 months ago by 43k • written 6.4 years ago by ▴ 130
15
votes
2
replies
6.9k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 14 months ago by 43k • written 11.6 years ago by 100k
2
votes
0
replies
6.8k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 11 months ago by 43k • written 6.3 years ago by ▴ 320
23
votes
19
replies
6.8k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 12 months ago by 43k • written 7.6 years ago by ★ 2.5k
21
votes
5
replies
6.8k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 12 months ago by 43k • written 7.8 years ago by ★ 1.5k
11
votes
0
replies
6.8k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 13 months ago by 43k • written 3.3 years ago by 141k
14
votes
31
replies
6.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 13 months ago by 43k • written 4.7 years ago by 8.5k
8
votes
12
replies
6.7k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 12 months ago by 43k • written 7.9 years ago by 13k
17
votes
0
replies
6.6k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 14 months ago by 43k • written 11.8 years ago by 100k
8
votes
2
replies
6.6k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 2.2 years ago by 43k • written 9.5 years ago by 12k
21
votes
9
replies
6.5k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 13 months ago by 43k • written 10.9 years ago by 9.7k
19
votes
7
replies
6.5k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 9 months ago by 81k • written 4.1 years ago by 6.3k
34
votes
15
replies
6.5k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 13 months ago by 43k • written 4.8 years ago by ★ 9.4k
14
votes
2
replies
6.5k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 12 months ago by 43k • written 8.6 years ago by ★ 3.9k
16
votes
6
replies
6.4k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 12 months ago by 43k • written 7.5 years ago by ★ 1.7k
6
votes
0
replies
6.4k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 14 months ago by 43k • written 11.9 years ago by ▴ 360
15
votes
7
replies
6.4k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 13 months ago by 43k • written 7.9 years ago by ★ 3.5k
20
votes
7
replies
6.3k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 13 months ago by 43k • written 5.5 years ago by ▴ 800
29
votes
5
replies
6.3k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 13 months ago by 43k • written 10.6 years ago by ★ 4.4k
13
votes
7
replies
6.1k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 13 months ago by 43k • written 3.6 years ago by 87k
4
votes
1
reply
6.1k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 14 months ago by 43k • written 12.0 years ago by ▴ 360
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 7 months ago by ▴ 20 • written 8.8 years ago by ▴ 430
22
votes
2
replies
6.0k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 12 months ago by 43k • written 7.5 years ago by ★ 2.1k
13
votes
6
replies
6.0k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 12 months ago by 43k • written 7.8 years ago by 14k
18
votes
2
replies
5.9k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 11 months ago by 43k • written 7.0 years ago by 5.3k
409 results • Page 3 of 9
Recent Votes
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
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Comment: Removing duplicates by joe ▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis by swbarnes2 14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file by swbarnes2 14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org by Ram 43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you so much
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org by Ram 43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you very much
Answer: Downloaded pdb's on rcsb.org by Ram 43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool by GenoMax 141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org by Ram 43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org by Ram 43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
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