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352 results • Page 3 of 8
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19
votes
9
replies
6.0k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 4 weeks ago by 38k • written 9.8 years ago by 9.5k
19
votes
4
replies
8.4k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 5 weeks ago by 38k • written 10.1 years ago by 97k
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 17 days ago by 38k • written 6.8 years ago by ▴ 170
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
kraken k-mer database python Tutorial
5.0 years ago by Sej Modha 5.2k
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 17 days ago by 38k • written 3.3 years ago by 7.8k
18
votes
2
replies
9.5k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 12 months ago by 38k • written 8.4 years ago by ▴ 860
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta Forum Tutorial
6.0 years ago by Michael D 52k
17
votes
3
replies
11k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 8 months ago by 38k • written 7.1 years ago by ★ 9.3k
16
votes
11
replies
7.3k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
17 days ago by Ram 38k
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 5 weeks ago by 38k • written 11.0 years ago by 9.9k
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 17 days ago by 38k • written 6.4 years ago by ★ 4.6k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 17 days ago by 38k • written 3.8 years ago by ▴ 310
16
votes
5
replies
8.4k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 5 weeks ago by 38k • written 10.5 years ago by 20k
15
votes
2
replies
1.4k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 5 months ago by ▴ 810 • written 18 months ago by ▴ 280
15
votes
1
reply
2.9k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
workshop training genomics lectures Tutorial
6.9 years ago by Malachi Griffith 19k
15
votes
5
replies
14k
views
Tutorial: How to create a mutation lolliplot with GenVisR
genvisr graphics bioconductor R Tutorial
updated 6.6 years ago by • 0 • written 6.8 years ago by 20k
15
votes
6
replies
5.7k
views
Tutorial: How to make your snakefiles self-documenting
snakemake Tutorial
updated 6.1 years ago by ★ 2.0k • written 6.4 years ago by ★ 1.7k
15
votes
2
replies
2.7k
views
Tutorial: Introduction to bedtools.
bedtools
updated 22 days ago by 38k • written 8.4 years ago by 11k
15
votes
1
reply
6.2k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
BED SAM psl blast Tutorial
5.4 years ago by Joseph Hughes ★ 3.0k
15
votes
0
replies
6.3k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 5 weeks ago by 38k • written 10.8 years ago by 97k
15
votes
4
replies
4.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 17 days ago by 38k • written 2.7 years ago by ▴ 300
15
votes
2
replies
6.5k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
15
votes
3
replies
4.2k
views
Tutorial: NCBI blast tutorial
ncbi blast tutorial Tutorial
updated 6.9 years ago by ▴ 540 • written 6.9 years ago by 11k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 22 days ago by 38k • written 5.3 years ago by ▴ 740
14
votes
2
replies
2.2k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R Tutorial
5.2 years ago by Jeremy Leipzig 21k
14
votes
0
replies
8.8k
views
Tutorial: How to generate PCA plot and heatmaps in R
RNA-Seq R PCA heatmap Tutorial
6.6 years ago by Ming Tommy Tang ★ 2.9k
14
votes
2
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 17 days ago by 38k • written 2.5 years ago by 2.9k
14
votes
2
replies
6.1k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 1 day ago by 38k • written 7.6 years ago by ★ 2.9k
14
votes
0
replies
7.9k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 12 months ago by 38k • written 8.2 years ago by ▴ 860
14
votes
7
replies
5.5k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 17 days ago by 38k • written 6.9 years ago by ★ 3.3k
13
votes
9
replies
4.1k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 9 months ago by ▴ 40 • written 16 months ago by ★ 1.1k
13
votes
6
replies
5.2k
views
Tutorial: Trim & align paired-end reads in a single pass
trim align paired-end fastq pipe Tutorial
6.8 years ago by dariober 14k
13
votes
8
replies
3.2k
views
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
4 months ago by ATpoint 71k
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 10 months ago by 38k • written 8.0 years ago by ▴ 860
12
votes
1
reply
4.8k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 17 days ago by 38k • written 3.0 years ago by 4.6k
12
votes
17
replies
2.2k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 3 months ago by 38k • written 7.8 years ago by 97k
12
votes
2
replies
1.0k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 17 days ago by 38k • written 2.0 years ago by 11k
12
votes
4
replies
1.8k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 8 days ago by 38k • written 5.6 years ago by ▴ 570
12
votes
11
replies
6.6k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI SRA Bioproject BioSample Tutorial
updated 5.7 years ago by ▴ 20 • written 6.1 years ago by ★ 2.4k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 17 days ago by 38k • written 3.8 years ago by ★ 14k
12
votes
1
reply
4.7k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 5 months ago by 38k • written 7.6 years ago by 3.5k
12
votes
4
replies
4.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 7 weeks ago by 38k • written 2.1 years ago by ▴ 120
12
votes
5
replies
7.6k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl Tutorial
6.5 years ago by Shicheng Guo ★ 9.3k
12
votes
1
reply
2.0k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 22 months ago by ★ 14k • written 22 months ago by 85k
12
votes
5
replies
1.8k
views
Tutorial: FASTA file split
fasta
updated 17 days ago by 38k • written 2.8 years ago by 7.8k
12
votes
0
replies
7.3k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 11 months ago by 38k • written 8.2 years ago by ★ 4.6k
12
votes
0
replies
2.1k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 17 days ago by 38k • written 2.6 years ago by 11k
12
votes
31
replies
4.8k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 22 days ago by 38k • written 3.6 years ago by 7.8k
11
votes
1
reply
2.2k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 17 days ago by 38k • written 2.2 years ago by ★ 23k
11
votes
1
reply
2.3k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 7 months ago by ★ 1.8k • written 14 months ago by 14k
352 results • Page 3 of 8
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Popular Question to zhou_1228 • 0
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Recent Replies
Comment: SKAT in R by Eliza ▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem by pinheirofabiano ▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic by antoine.fauchois92 • 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values by Eliza ▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate by Ram 38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis by rpolicastro 11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files by Darrenjdd • 0
Perfect! Thank you!
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