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55
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14
replies
93k
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10 follow
Tutorial: Using R in Conda
R
updated 14 months ago by 43k • written 3.8 years ago by ▴ 870
20
votes
14
replies
4.1k
views
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
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 15 months ago by 43k • written 11.3 years ago by 6.1k
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
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
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
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 29 days ago by 82k • written 4 weeks ago by ★ 1.7k
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 23 months ago by 82k
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
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
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
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
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
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
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
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
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
30
votes
10
replies
83k
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
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
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
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
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
16
votes
9
replies
7.2k
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
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
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
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
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
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
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
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
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
19
votes
7
replies
6.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 months ago by 82k • written 4.2 years ago by 6.4k
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
12
votes
7
replies
2.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
13 months ago by barslmn ★ 2.2k
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
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
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 15 months ago by 43k • written 11.7 years ago by 100k
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
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 14 months ago by 43k • written 10.3 years ago by 6.1k
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
46
votes
6
replies
25k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 2.3 years ago by ▴ 50 • written 3.2 years ago by 13k
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
106
votes
6
replies
26k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 14 months ago by 43k • written 5.7 years ago by 16k
412 results • Page 2 of 9
Recent Votes
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
Comment: Duplicated sequence samtools
Answer: Duplicated sequence samtools
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Recent Awards • All
Scholar to Pierre Lindenbaum 161k
Voter to Sara ▴ 30
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Recent Replies
Answer: Add stats to the plot by Ghada • 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot by GenoMax 142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files by Tommaso • 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot by Ghada • 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim() by ATpoint 82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis by LauferVA 4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2 by Ezequiel • 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot by marco.barr ▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
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