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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 ▴ 860
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 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
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
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
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
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
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
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
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
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 28 days ago by 82k • written 29 days ago by ★ 1.7k
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
12
votes
7
replies
2.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
13 months ago by barslmn ★ 2.2k
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
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
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
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
67
votes
6
replies
26k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 15 months ago by 43k • written 11.7 years ago by 100k
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
16
votes
6
replies
6.5k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 13 months ago by 43k • written 7.5 years ago by ★ 1.7k
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
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
412 results • Page 2 of 9
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Recent Replies
Answer: CellRanger output more cells than specified using --force-cells? Why? by scideas ▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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