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323 results • Page 2 of 7
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42
votes
19
replies
7.4k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 7 months ago by 40k • written 10.6 years ago by 4.1k
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 7 months ago by 40k • written 9.5 years ago by ★ 1.9k
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
39
votes
6
replies
18k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 4 months ago by 40k • written 6.1 years ago by ★ 3.3k
36
votes
5
replies
5.8k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 26 days ago by ▴ 20 • written 8.2 years ago by ▴ 410
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 5 months ago by 135k • written 9.9 years ago by 20k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 6 months ago by 40k • written 7.0 years ago by ▴ 310
34
votes
15
replies
5.8k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 6 months ago by 40k • written 4.3 years ago by ★ 9.3k
33
votes
9
replies
30k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 6 months ago by 40k • written 3.1 years ago by ▴ 160
32
votes
4
replies
7.1k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 6 months ago by 40k • written 4.9 years ago by ★ 1.6k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 6 months ago by 40k • written 3.4 years ago by 86k
31
votes
12
replies
28k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 7 months ago by 40k • written 10.0 years ago by 98k
31
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 7 months ago by 40k • written 9.5 years ago by ▴ 810
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 7 months ago by 40k • written 10.7 years ago by 6.0k
29
votes
5
replies
6.1k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 7 months ago by 40k • written 10.0 years ago by ★ 4.3k
28
votes
4
replies
4.1k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 6 months ago by 40k • written 4.7 years ago by 26k
27
votes
10
replies
70k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 6 months ago by 40k • written 2.5 years ago by ★ 1.4k
26
votes
0
replies
2.3k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 6 months ago by 40k • written 4.0 years ago by 19k
25
votes
15
replies
8.4k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 7 months ago by 40k • written 10.7 years ago by 9.7k
24
votes
4
replies
6.9k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 6 months ago by 40k • written 4.1 years ago by 77k
23
votes
19
replies
6.2k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 5 months ago by 40k • written 7.0 years ago by ★ 2.4k
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 5 months ago by 40k • written 6.9 years ago by ★ 2.1k
22
votes
1
reply
3.1k
views
Tutorial: Introduction To R Course Materials Available
R
updated 9 months ago by 40k • written 11.5 years ago by 26k
21
votes
10
replies
6.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 6 months ago by 40k • written 3.1 years ago by 12k
21
votes
9
replies
6.3k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 7 months ago by 40k • written 10.3 years ago by 9.7k
20
votes
14
replies
3.6k
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 6 months ago by 40k • written 7.4 years ago by ▴ 460
20
votes
5
replies
6.5k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 6 months ago by 40k • written 7.3 years ago by ★ 1.5k
20
votes
6
replies
5.2k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 6 months ago by 40k • written 7.0 years ago by ★ 5.2k
20
votes
2
replies
7.6k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 4 months ago by 40k • written 5.9 years ago by ★ 3.4k
20
votes
4
replies
2.4k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 6 months ago by 40k • written 4.4 years ago by ▴ 180
20
votes
7
replies
6.0k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 6 months ago by 40k • written 5.0 years ago by ▴ 760
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 7 months ago by 40k • written 10.5 years ago by 20k
20
votes
0
replies
8.5k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 5 months ago by 40k • written 7.1 years ago by ★ 4.2k
19
votes
13
replies
6.9k
views
9 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 4 days ago by 14k • written 15 months ago by 77k
19
votes
4
replies
8.6k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 7 months ago by 40k • written 10.6 years ago by 98k
19
votes
2
replies
3.2k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 4 months ago by 40k • written 6.5 years ago by ▴ 640
18
votes
22
replies
8.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 11 days ago by ▴ 20 • written 3.8 years ago by 8.3k
18
votes
7
replies
5.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 11 weeks ago by 77k • written 3.5 years ago by 5.5k
18
votes
2
replies
5.7k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 4 months ago by 40k • written 6.4 years ago by 5.2k
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 6 months ago by 40k • written 7.3 years ago by ▴ 170
17
votes
13
replies
1.9k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 4 months ago by 40k • written 6.5 years ago by 53k
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 7 months ago by 40k • written 11.5 years ago by 10k
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 6 months ago by 40k • written 6.9 years ago by ★ 4.7k
16
votes
11
replies
7.7k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
6 months ago by Ram 40k
16
votes
5
replies
8.7k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 7 months ago by 40k • written 11.0 years ago by 20k
16
votes
7
replies
14k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 6 months ago by 40k • written 4.3 years ago by ▴ 310
16
votes
0
replies
6.5k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 7 months ago by 40k • written 11.3 years ago by 98k
16
votes
6
replies
6.1k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 5 months ago by 40k • written 6.9 years ago by ★ 1.7k
323 results • Page 2 of 7
Recent Votes
Comment: rRNA contamination in RNAseq datasets
Imputation server failing to see samples in VCF files
Answer: Imputation server failing to see samples in VCF files
Need help to setup a PGS pipeline
rRNA detection (for contamination) in RNA-seq
A: rRNA detection (for contamination) in RNA-seq
Comment: Finding sequences in unannotated genomes using reference coordinates
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Recent Replies
Comment: pheatmap by Sara ▴ 30
Thank you for your comment, but it did not help!
Comment: 18S taxonomy assignment SILVA database formatting by antonioggsousa 2.8k
Please, whenever you need to add more information, just edit your original post and do not add answers below unless you found the solution …
Comment: Clustalo failing to complete multiple sequence alignments by saamhasan55 ▴ 10
Hi, I know this is an old thread, but I am encountering a similar problem. I am trying to do an msa for the cds sequences of 5 bumblebee sp…
Comment: 18S taxonomy assignment SILVA database formatting by antonioggsousa 2.8k
Hi! Please share first with us an example how the data looks like, the command-line you're running and the problem that you're getting. If…
Answer: Finding sequences in unannotated genomes using reference coordinates by Prangan ▴ 20
I may have stumbled on a solution for this problem. What I wanted was the SNPs or mutations in the VCF to be incorporated in the reference.…
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset by prietto • 0
Thank you. I tried doing a pseudobulk analysis by doing the following: I have 9 patient ids in a column `Patient` in my metadata, and a co…
Comment: STAR Genome index Error by ATpoint 77k
How much memory does you machine have?
Comment: tximport error: vroom by ATpoint 77k
It's a problem with the import of the text files (quant.sf) I would say. I cannot really debug the error itself, but can you try ```r …
Comment: Converting from BED to SAF/GFF by ATpoint 77k
It's recommended to make a `Tool` post with usage examples that you can link to.
Answer: Error in checkFullRank(modelMatrix) : by ATpoint 77k
Sample is nested with condition and with itself, meaning that each sample is either condition1 or 2, but for a paired design each sample wo…
Comment: The Biostar Handbook. A bioinformatics e-book for beginners. by Michael 53k
Software carpentry provides some good [introductory courses in Linux, Git, Python and R][1]. We are using these materials in our local soft…
Comment: How to get sample names and genotype for SNP in multi-sample VCF file by Kevin Blighe 86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF by alejandrogzi ▴ 40
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF by alejandrogzi ▴ 40
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other by alejandrogzi ▴ 40
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
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