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411 results • Page 2 of 9
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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 Windows EaSeq
updated 12 months ago by 43k • written 8.0 years ago by ▴ 460
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 14 months ago by 43k • written 11.2 years ago by 6.0k
54
votes
14
replies
91k
views
10 follow
Tutorial: Using R in Conda
R
updated 13 months ago by 43k • written 3.8 years ago by ▴ 850
76
votes
14
replies
16k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
9
votes
14
replies
3.7k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 18 months ago by ▴ 10 • written 2.2 years ago by ▴ 40
35
votes
13
replies
14k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 2.3 years ago by ★ 1.4k • written 2.5 years ago by 100k
64
votes
13
replies
13k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 2.2 years ago by 43k • written 9.5 years ago by ★ 2.4k
75
votes
13
replies
67k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 18 months ago by 43k • written 10.4 years ago by ★ 1.2k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 6 weeks ago by • 0 • written 3.6 years ago by 3.2k
18
votes
13
replies
2.2k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 11 months ago by 43k • written 7.1 years ago by 54k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 10 months ago by 43k • written 5.2 years ago by ▴ 170
77
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.5 years ago by 43k • written 9.9 years ago by 19k
21
votes
13
replies
10k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 months ago by • 0 • written 22 months ago by 82k
5
votes
13
replies
1.2k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 7 days ago by 82k • written 8 days ago by ★ 1.7k
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
34
votes
12
replies
30k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 14 months ago by 43k • written 10.5 years ago by 100k
16
votes
11
replies
8.3k
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
6
votes
11
replies
5.7k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 14 months ago by 43k • written 7.4 years ago by ▴ 50
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 13 months ago by 43k • written 7.5 years ago by ★ 4.7k
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
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 3.7 years ago by 13k
6
votes
10
replies
5.2k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 13 months ago by 43k • written 6.2 years ago by ▴ 370
30
votes
10
replies
81k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 13 months ago by 43k • written 3.1 years ago by ★ 1.6k
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
66
votes
9
replies
49k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 14 months ago by 43k • written 10.8 years ago by ★ 3.0k
21
votes
9
replies
6.5k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 11 months ago by 43k • written 6.6 years ago by 87k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 13 months ago by 43k • written 10.0 years ago by ★ 1.9k
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 13 months ago by 43k • written 10.0 years ago by ★ 1.8k
7
votes
8
replies
3.4k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 16 months ago by 43k • written 8.8 years ago by ★ 2.3k
81
votes
8
replies
8.6k
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
23
votes
8
replies
5.4k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 2.3 years ago by 43k • written 9.7 years ago by 24k
99
votes
8
replies
29k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 12 months ago by 43k • written 8.2 years ago by ★ 1.1k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 13 months ago by 43k • written 10.0 years ago by ▴ 810
16
votes
7
replies
16k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 13 months ago by 43k • written 4.9 years ago by ▴ 310
11
votes
7
replies
2.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
13 months ago by barslmn ★ 2.1k
13
votes
7
replies
6.2k
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
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 11 months ago by 43k • written 3.2 years ago by ▴ 420
20
votes
7
replies
6.4k
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
8
votes
7
replies
8.4k
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
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 11 months ago by 43k • written 6.6 years ago by 87k
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
19
votes
7
replies
6.6k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 9 months ago by 82k • written 4.1 years ago by 6.4k
50
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 14 months ago by 43k • written 11.7 years ago by 100k
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
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 7.9 years ago by 14k
30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 19 months ago by 43k • written 12.0 years ago by 100k
106
votes
6
replies
26k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 13 months ago by 43k • written 5.7 years ago by 16k
32
votes
6
replies
12k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 13 months ago by 43k • written 3.9 years ago by 87k
2
votes
6
replies
3.2k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 12 months ago by 43k • written 7.8 years ago by ▴ 140
411 results • Page 2 of 9
Recent Votes
NGS forensics: how to know if data is fabricated
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
How do I find out the read lenght of a fastq file?
Calculate Allele balance by sample
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
Answer: Is there a tool that sorts gtf files?
Answer: gvcf joint calling
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Answer: NGS forensics: how to know if data is fabricated by Jeremy Leipzig 22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
Answer: absolute path for symbolic links in Snakefile by Jesse ▴ 740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in by Jesse ▴ 740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
Comment: Source other conda environments in a nextflow pipeline when nextflow itself is i by Arup Ghosh 3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling by Jeremy Leipzig 22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by O.rka ▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i by colindaven 6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
Comment: different FeatureCounts output for the same data by Istvan Albert 100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question by starswillfade ▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling by zihanss • 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Guille • 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq by dsull ★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
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