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231 results • Page 3 of 5
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4
votes
1
reply
5.8k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 5 weeks ago by 38k • written 10.9 years ago by ▴ 360
20
votes
7
replies
5.6k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 17 days ago by 38k • written 4.5 years ago by ▴ 740
34
votes
4
replies
5.5k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 4 months ago by 38k • written 7.7 years ago by ▴ 370
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
6
votes
3
replies
5.4k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 5 weeks ago by 38k • written 10.7 years ago by 97k
7
votes
0
replies
5.1k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 5 weeks ago by 38k • written 10.8 years ago by ▴ 120
34
votes
15
replies
5.1k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 17 days ago by 38k • written 3.8 years ago by ★ 9.3k
3
votes
2
replies
4.9k
views
Tutorial: Reorder Vcf Files
vcf
updated 5 weeks ago by 38k • written 9.9 years ago by ▴ 60
20
votes
6
replies
4.8k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 17 days ago by 38k • written 6.5 years ago by ★ 5.2k
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
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
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
20
votes
10
replies
4.7k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 17 days ago by 38k • written 2.6 years ago by 11k
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
3
votes
0
replies
4.5k
views
Tutorial: Comparing 454, Iontorrent And Miseq
454 miseq ion-torrent
updated 5 weeks ago by 38k • written 10.9 years ago by 97k
11
votes
6
replies
4.5k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 8 months ago by 38k • written 7.1 years ago by ★ 4.1k
6
votes
11
replies
4.5k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 7 weeks ago by 38k • written 6.3 years ago by ▴ 50
11
votes
7
replies
4.5k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 17 days ago by 38k • written 2.5 years ago by 85k
10
votes
0
replies
4.5k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 17 days ago by 38k • written 2.2 years ago by 127k
7
votes
0
replies
4.5k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 28 days ago by 38k • written 9.1 years ago by ▴ 990
5
votes
3
replies
4.5k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 15 days ago by • 0 • written 5.4 years ago by ▴ 130
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
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 17 days ago by 38k • written 5.1 years ago by ▴ 340
10
votes
3
replies
4.1k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 10 weeks ago by 38k • written 8.5 years ago by ▴ 860
9
votes
0
replies
4.1k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 8 months ago by 38k • written 7.2 years ago by 19k
6
votes
3
replies
4.1k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 16 days ago by 38k • written 4.4 years ago by ▴ 40
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
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
50
votes
3
replies
4.0k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 17 days ago by 38k • written 4.2 years ago by 71k
5
votes
1
reply
3.9k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 3 months ago by 38k • written 7.8 years ago by 7.7k
5
votes
3
replies
3.9k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 5 weeks ago by 38k • written 10.3 years ago by ▴ 80
9
votes
3
replies
3.9k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
4
votes
3
replies
3.9k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 17 days ago by 38k • written 5.0 years ago by ★ 3.9k
2
votes
0
replies
3.8k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 17 days ago by 38k • written 3.7 years ago by ▴ 20
21
votes
2
replies
3.7k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 6 months ago by ▴ 40 • written 23 months ago by 7.8k
28
votes
4
replies
3.7k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 16 days ago by 38k • written 4.2 years ago by 26k
1
vote
0
replies
3.5k
views
Tutorial: embarrassingly easy parallel in Python, Perl and R
parallel
updated 7 months ago by 38k • written 7.4 years ago by ▴ 70
5
votes
0
replies
3.5k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
updated 17 days ago by 38k • written 2.2 years ago by 127k
3
votes
0
replies
3.4k
views
Tutorial: Video Tutorial On Conducting Whole-Exome Sequencing Research
exome-sequencing
updated 4 weeks ago by 38k • written 9.8 years ago by 9.5k
6
votes
0
replies
3.4k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 25 days ago by 38k • written 8.8 years ago by 7.7k
4
votes
2
replies
3.3k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 16 days ago by 38k • written 7.1 years ago by ★ 2.4k
7
votes
2
replies
3.3k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 5 weeks ago by 38k • written 10.5 years ago by 11k
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
10
votes
2
replies
3.1k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 7 months ago by 38k • written 7.4 years ago by 20k
4
votes
1
reply
3.0k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 5 weeks ago by 38k • written 10.9 years ago by ▴ 360
7
votes
8
replies
3.0k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 3 months ago by 38k • written 7.7 years ago by ★ 2.2k
6
votes
0
replies
3.0k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 5 weeks ago by 38k • written 10.9 years ago by 26k
22
votes
1
reply
3.0k
views
Tutorial: Introduction To R Course Materials Available
R
updated 12 weeks ago by 38k • written 10.9 years ago by 26k
1
vote
2
replies
2.9k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 5 months ago by 38k • written 7.7 years ago by ▴ 10
1
vote
0
replies
2.9k
views
Tutorial: Canadian Bioinformatics Workshops 2016 Series
Assembly SNP RNA-Seq ChIP-Seq alignment
updated 9 months ago by 38k • written 7.2 years ago by ▴ 30
231 results • Page 3 of 5
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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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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