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Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization EaSeq Tutorial Windows
6.9 years ago by Mads Lerdrup ▴ 460
30
votes
14
replies
15k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 5 weeks ago by 38k • written 10.2 years ago by 5.9k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 18 days ago by 38k • written 2.7 years ago by ▴ 690
7
votes
14
replies
2.1k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 5 months ago by • 0 • written 13 months ago by ▴ 30
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
74
votes
13
replies
65k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 5 months ago by 38k • written 9.4 years ago by ★ 1.2k
25
votes
13
replies
6.9k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 14 months ago by ★ 1.2k • written 17 months ago by 97k
63
votes
13
replies
12k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 13 months ago by 38k • written 8.4 years ago by ★ 2.3k
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 17 months ago by 38k • written 8.8 years ago by 19k
3
votes
13
replies
9.5k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 23 days ago by 38k • written 4.1 years ago by ▴ 140
8
votes
12
replies
6.1k
views
Tutorial: Create your own VPN to access work resources from home
VPN OpenVPN tinyproxy Tutorial
6.8 years ago by John 13k
31
votes
12
replies
26k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 4 weeks ago by 38k • written 9.5 years ago by 97k
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
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
18 days ago by Ram 38k
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 18 days ago by 38k • written 6.4 years ago by ★ 4.6k
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
26
votes
10
replies
59k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 23 days ago by 38k • written 2.0 years ago by ★ 1.3k
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 18 days ago by 38k • written 2.6 years ago by 11k
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 18 days ago by 38k • written 5.1 years ago by ▴ 340
9
votes
9
replies
3.7k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
ngs reference coverage Tutorial
updated 5.5 years ago by 103k • written 5.5 years ago by 85k
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
31
votes
9
replies
24k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 18 days ago by 38k • written 2.6 years ago by ▴ 140
65
votes
9
replies
47k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 weeks ago by 38k • written 9.8 years ago by ★ 3.0k
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
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 26 days ago by 38k • written 9.0 years ago by ★ 1.8k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 26 days ago by 38k • written 9.0 years ago by ★ 1.9k
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
TCGA cancer tools RNA-Seq clinical Tutorial
updated 6.3 years ago by ▴ 250 • written 7.1 years ago by ★ 1.1k
81
votes
8
replies
7.8k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 26 days ago by 38k • written 8.8 years ago by 19k
37
votes
8
replies
9.3k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 23 days ago by 38k • written 2.5 years ago by 2.9k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 26 days ago by 38k • written 9.0 years ago by ▴ 800
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 7.8 years ago by ★ 2.2k
23
votes
8
replies
4.9k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 15 months ago by 38k • written 8.6 years ago by 24k
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
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 18 days ago by 38k • written 6.9 years ago by ★ 3.3k
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 18 days ago by 38k • written 4.5 years ago by ▴ 740
10
votes
7
replies
1.1k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
2 days ago by barslmn ★ 1.4k
8
votes
7
replies
7.7k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 14 months ago by 38k • written 9.3 years ago by ★ 2.6k
11
votes
7
replies
4.5k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 18 days ago by 38k • written 2.5 years ago by 85k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 18 days ago by 38k • written 3.8 years ago by ▴ 310
48
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
9
votes
7
replies
6.1k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 6 months ago by • 0 • written 2.1 years ago by ▴ 240
10
votes
7
replies
13k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk bash duplicates linux Tutorial
updated 5.6 years ago by 34k • written 5.6 years ago by 85k
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 4 weeks ago by 38k • written 9.2 years ago by 5.9k
67
votes
6
replies
24k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
60
votes
6
replies
8.9k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 4 weeks ago by 38k • written 9.6 years ago by 9.5k
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
2
votes
6
replies
2.8k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
R gene Tutorial Rembrandt
updated 5.9 years ago by • 0 • written 6.7 years ago by ▴ 140
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
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
31
votes
6
replies
8.8k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 18 days ago by 38k • written 2.9 years ago by 85k
352 results • Page 2 of 8
Recent Votes
Answer: Sequence statistics to report viruses (or bacteria and fungi) using Nanopore for
Answer: Sequence statistics to report viruses (or bacteria and fungi) using Nanopore for
Answer: how can i filter a sam file from a paf file
Answer: Align miRNA library (small RNA-seq) without trimming
Answer: Snakemake workflow for trimmomatic
C: Adjust for covariates
Comment: syntax errors when running part3 all-against-all
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Recent Replies
Answer: Getting Intron Positions from Amino Acid Sequences by fafad046 • 0
Do you happen to know why sometimes my Entrez direct command gives no output at all? I installed Entrez direct using the commands listed…
Comment: Getting Intron Positions from Amino Acid Sequences by fafad046 • 0
Do you happen to know why sometimes my Entrez direct command gives no output at all? I installed Entrez direct using the commands listed o…
Comment: Diffbind dba.count doesn't give FRiP score by gyspace • 0
I found your email in https://bioinfotraining.bio.cam.ac.uk/staff/rory-stark-phd, is the email right? I sent a google drive link to you. If…
Comment: how can i filter a sam file from a paf file by colindaven 4.7k
Just save yourself a lot of pain and learn to filter the sam/bam file efficiently. It is much more of a widespread standard than PAF.
Comment: Snakemake workflow for trimmomatic by GenoMax 127k
Please accept this answer (green check mark) to provide closure to this thread.
Comment: syntax errors when running part3 all-against-all by Sofia • 0
When I started with the gz all-vs-all files for CHICK and ANOCA and started oma, everything ran fine, I got output. Then, in the same direc…
Comment: Quality control of Chip-seq data (NRF and PCB) by michelafrancesconi9 • 0
Can you explain me better? Because for the NRF I do : a) samtools view -c .bam b)samtools view -c -F 260 .bam then b/a and as a bam fi…
Comment: pyCirclize - Circular visualization in Python by karenkvn ▴ 40
Thank you for responding so quickly - this works perfectly!
Comment: pyCirclize - Circular visualization in Python by moshi ▴ 110
Please install Biopython with v1.80 or higher. If biopython>=1.80, there should be no errors.
Comment: Gene family classification using RNA-seq data by Dion • 0
well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual pack…
Comment: pyCirclize - Circular visualization in Python by karenkvn ▴ 40
Thank you for this wonderful programme! I am plotting a bacterial chromosome and find that when I plot the NC_000913 chromosome using the e…
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…
Comment: 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…
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