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356 results • Page 3 of 8
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19
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2
replies
3.1k
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Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 22 days ago by 39k • written 6.2 years ago by ▴ 640
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
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 11 weeks ago by 39k • written 6.9 years ago by ▴ 170
18
votes
3
replies
12k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 10 months ago by 39k • written 7.3 years ago by ★ 9.3k
18
votes
22
replies
7.5k
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
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 21 days ago by 39k • written 6.1 years ago by 5.2k
18
votes
2
replies
9.6k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 14 months ago by 39k • written 8.6 years ago by ▴ 860
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 22 days ago by 39k • written 6.2 years ago by 52k
16
votes
7
replies
13k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 11 weeks ago by 39k • written 4.0 years ago by ▴ 310
16
votes
11
replies
13k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 11 weeks ago by 39k • written 6.6 years ago by ★ 4.6k
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 3 months ago by 39k • written 11.2 years ago by 9.9k
16
votes
9
replies
4.6k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 11 months ago by ▴ 70 • written 18 months ago by ★ 1.1k
16
votes
5
replies
8.5k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 3 months ago by 39k • written 10.7 years ago by 20k
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
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
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 12 weeks ago by 39k • written 5.5 years ago by ▴ 750
15
votes
4
replies
4.2k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 310
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
15
votes
5
replies
14k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 8 weeks ago by 39k • written 7.0 years ago by 20k
15
votes
1
reply
2.9k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 8 weeks ago by 39k • written 7.1 years ago by 19k
15
votes
2
replies
1.6k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 7 months ago by ▴ 810 • written 20 months ago by ▴ 280
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 16 days ago by 39k • written 5.6 years ago by ★ 3.0k
15
votes
3
replies
4.3k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 8 weeks ago by 39k • written 7.1 years ago by 11k
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
15
votes
2
replies
2.7k
views
Tutorial: Introduction to bedtools.
bedtools
updated 12 weeks ago by 39k • written 8.5 years ago by 12k
14
votes
9
replies
4.2k
views
6 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 29 days ago by • 0 • written 11 months ago by 72k
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
14
votes
2
replies
3.0k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 11 weeks ago by 39k • written 2.7 years ago by 2.9k
14
votes
2
replies
2.2k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R
updated 8 weeks ago by 39k • written 7.2 years ago by 21k
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
14
votes
0
replies
8.9k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 2.9k
14
votes
0
replies
8.0k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 14 months ago by 39k • written 8.4 years ago by ▴ 860
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
13
votes
3
replies
4.7k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 12 months ago by 39k • written 8.2 years ago by ▴ 860
12
votes
1
reply
5.0k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 11 weeks ago by 39k • written 3.2 years ago by 4.8k
12
votes
17
replies
2.3k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 5 months ago by 39k • written 8.0 years ago by 98k
12
votes
5
replies
1.9k
views
Tutorial: FASTA file split
fasta
updated 11 weeks ago by 39k • written 3.0 years ago by 7.9k
12
votes
1
reply
4.7k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 7 months ago by 39k • written 7.8 years ago by 3.5k
12
votes
7
replies
4.8k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 11 weeks ago by 39k • written 2.7 years ago by 85k
12
votes
20
replies
12k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 11 weeks ago by 39k • written 4.0 years ago by ★ 14k
12
votes
4
replies
4.7k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 3 months ago by 39k • written 2.3 years ago by ▴ 120
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 23 days ago by 39k • written 6.2 years ago by ★ 2.4k
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
12
votes
1
reply
2.6k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 9 months ago by ★ 1.8k • written 17 months ago by 14k
12
votes
0
replies
2.2k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 11 weeks ago by 39k • written 2.8 years ago by 12k
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
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
12
votes
1
reply
2.2k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 24 months ago by ★ 14k • written 24 months ago by 85k
12
votes
4
replies
1.9k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 10 weeks ago by 39k • written 5.7 years ago by ▴ 590
12
votes
2
replies
1.1k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 11 weeks ago by 39k • written 2.2 years ago by 12k
356 results • Page 3 of 8
Recent Votes
Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Recent Replies
Comment: Low mapping percentage by Sib ▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data by Hamid Ghaedi 2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP by Vincent Laufer ★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs by rycro_c • 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage by Dave Carlson ★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order? by Pierre Lindenbaum 154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage by GenoMax 129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files by Joe 21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig by GenoMax 129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order? by GenoMax 129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column by atemedorri137798 • 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order? by Ram 39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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