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30
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14
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14k
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8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
install genome music linux smg Tutorial
6.3 years ago by Cyriac Kandoth 5.8k
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 15 months ago by 37k • written 8.7 years ago by 19k
53
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 4 months ago by 37k • written 9.2 years ago by ★ 1.2k
15
votes
5
replies
13k
views
Tutorial: How to create a mutation lolliplot with GenVisR
genvisr graphics bioconductor R Tutorial
updated 6.4 years ago by • 0 • written 6.6 years ago by 20k
74
votes
14
replies
13k
views
15 follow
Tutorial: List Of Bioinformatics Books
bioinformatics tutorial books Tutorial
updated 4 months ago by 37k • written 9.7 years ago by 9.5k
79
votes
21
replies
13k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment Tutorial GSEA RNA-Seq
6 weeks ago by Hamid Ghaedi 2.8k
16
votes
11
replies
13k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
cBioportal TCGA data_retrieval RNASeq R Tutorial
updated 3.7 years ago by ▴ 30 • written 6.3 years ago by ★ 4.6k
10
votes
7
replies
13k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk bash duplicates linux Tutorial
updated 5.4 years ago by 34k • written 5.4 years ago by 84k
20
votes
4
replies
13k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix tutorial Tutorial
updated 4.5 years ago by ▴ 10 • written 9.9 years ago by 20k
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
rna-seq analysis tutorial Tutorial
updated 10.5 years ago by 3.8k • written 10.8 years ago by 9.8k
63
votes
13
replies
12k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 11 months ago by 37k • written 8.2 years ago by ★ 2.3k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
orthomcl mysql no root local Tutorial
updated 11 months ago by 37k • written 8.2 years ago by ▴ 580
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 18 days ago by 37k • written 9.9 years ago by 96k
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational biology Tutorial
6.8 years ago by Sinji ★ 3.2k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
Seurat clonotyping VDJ sc-RNAseq Tutorial
updated 23 months ago by 8.6k • written 3.6 years ago by ▴ 310
1
vote
1
reply
11k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 6 months ago by ★ 2.5k • written 6 months ago by ▴ 10
64
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
R Tutorial biocparallel mclapply foreach
3.2 years ago by Kevin Blighe 84k
57
votes
15
replies
11k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
4.2 years ago by finswimmer 15k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
20 months ago by jared.andrews07 ★ 14k
41
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf vcf ensembl tcga somatic Tutorial
2.1 years ago by Cyriac Kandoth 5.8k
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 6 months ago by 37k • written 7.0 years ago by ★ 1.8k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr gene RNA-Seq R Tutorial
updated 8 months ago by 84k • written 5.2 years ago by ▴ 740
17
votes
3
replies
11k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 6 months ago by 37k • written 7.0 years ago by ★ 9.2k
48
votes
7
replies
10k
views
7 follow
Tutorial: Genome Assembly Review Papers
papers assembly tutorial Tutorial
updated 9.9 years ago by 33k • written 10.4 years ago by 96k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell Tutorial flow-cytometry
9 weeks ago by Ahill ★ 1.9k
64
votes
26
replies
10k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 20 months ago by ▴ 180 • written 3.9 years ago by 15k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 9 months ago by 37k • written 8.8 years ago by ★ 1.8k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
bioinformatics pipeline python tutorial Tutorial
updated 8 months ago by 37k • written 8.8 years ago by ▴ 800
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
Tutorial fasta fastq
updated 16 months ago by 37k • written 8.8 years ago by ★ 1.8k
18
votes
2
replies
9.5k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 10 months ago by 37k • written 8.3 years ago by ▴ 860
60
votes
6
replies
8.8k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line tools bioinformatics Tutorial
updated 10 weeks ago by 37k • written 9.5 years ago by 9.5k
3
votes
13
replies
8.8k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf merge bcftools Tutorial
written 3.9 years ago by ▴ 140
14
votes
0
replies
8.7k
views
Tutorial: How to generate PCA plot and heatmaps in R
RNA-Seq R PCA heatmap Tutorial
6.4 years ago by Ming Tang ★ 2.9k
37
votes
8
replies
8.6k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer Tutorial R methylation
updated 8 weeks ago by ★ 1.1k • written 2.3 years ago by 2.8k
9
votes
4
replies
8.5k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long reads minion oxford nanopore Tutorial
2.9 years ago by colindaven 4.4k
19
votes
4
replies
8.3k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
rna-seq tutorial Tutorial
6.1 years ago by Istvan Albert 96k
19
votes
0
replies
8.3k
views
Tutorial: Metagenomics Review Papers
papers metagenomics tutorial Tutorial
10.0 years ago by Istvan Albert 96k
16
votes
5
replies
8.3k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
biomart perl api tutorial Tutorial
updated 4 months ago by 37k • written 10.4 years ago by 20k
9
votes
23
replies
8.2k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
orthomcl ubuntu linux mysql Tutorial
4.7 years ago by vimalkvn ▴ 310
20
votes
4
replies
8.1k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR Tutorial
6.4 years ago by fi1d18 ★ 4.1k
31
votes
6
replies
8.0k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
17 months ago by Kevin Blighe 84k
9
votes
0
replies
8.0k
views
Tutorial: Installing And Running Ncbi Blast
blast tutorial tutorial Tutorial
10.8 years ago by MSU course 2011 ▴ 540
14
votes
0
replies
7.9k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 10 months ago by 37k • written 8.0 years ago by ▴ 860
24
votes
15
replies
7.8k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
bioinformatics training tutorial Tutorial
10 months ago by Medhat 9.5k
0
votes
0
replies
7.7k
views
Tutorial: Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter Python pattern
12 months ago by Wayne ★ 1.5k
81
votes
8
replies
7.7k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
genomics workshop Tutorial lectures training
updated 8 months ago by 37k • written 8.6 years ago by 19k
3
votes
3
replies
7.6k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
sra fastq sam Aspera Connect Tutorial
5.1 years ago by Wenhu_Cao ▴ 100
8
votes
7
replies
7.6k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 11 months ago by 37k • written 9.2 years ago by ★ 2.6k
6
votes
1
reply
7.5k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
rna-seq tophat cufflinks tutorial Tutorial
10.7 years ago by Istvan Albert 96k
2
votes
2
replies
7.5k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
UMI FASTQ fastp Tutorial
5.2 years ago by chen ★ 2.4k
353 results • Page 2 of 8
Recent Votes
Comment: a problem with getBM
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
Answer: Gene Set Enrichment Analysis, pathway, metabolism
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Recent Replies
Answer: a problem with getBM by sanaz • 0
head(ensembl_ids) X baseMean log2FoldChange lfcS…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v by fuellen ▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM by Mike Smith ★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome by congliu37 • 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File? by Jeremy Leipzig 21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)? by Fabio Marroni ★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism by Rob ▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers by Pierre Lindenbaum 152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence by vvasta • 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation? by Fabio Marroni ★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2 by Fabio Marroni ★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file** by Pierre Lindenbaum 152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4 by Pierre Lindenbaum 152k
I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of gzip < chr1.vcf.gz > chr1.vcf.gz…
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