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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 13 months ago by 43k • written 8.0 years ago by ▴ 460
55
votes
14
replies
93k
views
10 follow
Tutorial: Using R in Conda
R
updated 14 months ago by 43k • written 3.8 years ago by ▴ 860
76
votes
14
replies
16k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 15 months ago by 43k • written 11.0 years ago by 9.7k
9
votes
14
replies
3.8k
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
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 11.3 years ago by 6.1k
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 2.3 years ago by 43k • written 9.5 years ago by ★ 2.4k
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 2.6 years ago by 100k
77
votes
13
replies
16k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.6 years ago by 43k • written 10.0 years ago by 20k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 9 weeks ago by • 0 • written 3.6 years ago by 3.2k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 11 months ago by 43k • written 5.2 years ago by ▴ 170
18
votes
13
replies
2.2k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 12 months ago by 43k • written 7.1 years ago by 54k
5
votes
13
replies
2.0k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 26 days ago by 82k • written 27 days ago by ★ 1.7k
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 10.5 years ago by ★ 1.2k
21
votes
13
replies
11k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 6 months ago by • 0 • written 22 months ago by 82k
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 10.6 years ago by 100k
8
votes
12
replies
6.8k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 13 months ago by 43k • written 8.0 years ago by 13k
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
14 months ago by Ram 43k
12
votes
11
replies
7.6k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 12 months ago by 43k • written 7.2 years ago by ★ 2.4k
6
votes
11
replies
5.7k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 15 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 14 months ago by 43k • written 7.6 years ago by ★ 4.7k
6
votes
10
replies
5.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 14 months ago by 43k • written 6.2 years ago by ▴ 380
30
votes
10
replies
82k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 14 months ago by 43k • written 3.2 years ago by ★ 1.6k
22
votes
10
replies
7.1k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 14 months ago by 43k • written 3.7 years ago by 13k
66
votes
9
replies
49k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 15 months ago by 43k • written 10.9 years ago by ★ 3.0k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 14 months ago by 43k • written 10.1 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 14 months ago by 43k • written 10.1 years ago by ★ 1.8k
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 12 months ago by 43k • written 6.7 years ago by 88k
21
votes
9
replies
6.6k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
16
votes
9
replies
7.1k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 23 months ago by ▴ 70 • written 2.5 years ago by ★ 1.3k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 14 months ago by 43k • written 10.1 years ago by ▴ 810
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 14 months ago by 43k • written 9.9 years ago by 20k
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 17 months ago by 43k • written 8.9 years ago by ★ 2.3k
23
votes
8
replies
5.4k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 2.4 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 13 months ago by 43k • written 8.2 years ago by ★ 1.1k
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 14 months ago by 43k • written 5.6 years ago by ▴ 800
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 12 months ago by 43k • written 3.2 years ago by ▴ 420
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 12 months ago by 43k • written 6.7 years ago by 88k
13
votes
7
replies
6.3k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 14 months ago by 43k • written 3.7 years ago by 88k
8
votes
7
replies
8.4k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 2.3 years ago by 43k • written 10.5 years ago by ★ 2.6k
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
11
votes
7
replies
2.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
13 months ago by barslmn ★ 2.1k
15
votes
7
replies
6.5k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 14 months ago by 43k • written 8.0 years ago by ★ 3.5k
16
votes
7
replies
16k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 14 months ago by 43k • written 4.9 years ago by ▴ 310
19
votes
7
replies
6.6k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 months ago by 82k • written 4.1 years ago by 6.4k
13
votes
6
replies
6.0k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 13 months ago by 43k • written 7.9 years ago by 14k
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 7 weeks ago by 43k • written 6.2 years ago by 88k
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 13 months ago by 43k • written 7.9 years ago by ▴ 140
30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 20 months ago by 43k • written 12.1 years ago by 100k
61
votes
6
replies
9.5k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by 43k • written 10.8 years ago by 9.7k
32
votes
6
replies
12k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 14 months ago by 43k • written 4.0 years ago by 88k
412 results • Page 2 of 9
Recent Votes
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index by Lorenzo • 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED? by dthorbur ★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto by dariober 14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err by GenoMax 142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input? by Pierre Lindenbaum 161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
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