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12
votes
5
replies
9.3k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr gene RNA-Seq R Tutorial
updated 12 days ago by 81k • written 4.5 years ago by ▴ 610
0
votes
0
replies
276
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
TCGA Counts v32.0 Biolinks GDC STAR
5 weeks ago by dare_devil ★ 1.5k
29
votes
3
replies
6.2k
views
7 follow
Tutorial: Methylation Analysis Tutorial in R_part1
Tutorial cancer methylation R
updated 6 weeks ago by 115k • written 19 months ago by ★ 2.5k
1
vote
2
replies
344
views
Tutorial: Running fastq_screen on your data
fastqscreen
8 weeks ago by rohitsatyam102 ▴ 460
7
votes
12
replies
865
views
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 11 weeks ago by ▴ 620 • written 12 weeks ago by ▴ 30
68
votes
14
replies
12k
views
15 follow
Tutorial: List Of Bioinformatics Books
bioinformatics tutorial books Tutorial
updated 12 weeks ago by ▴ 40 • written 9.0 years ago by 9.3k
21
votes
13
replies
2.4k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 3 months ago by ▴ 870 • written 7 months ago by 93k
3
votes
13
replies
6.3k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf merge bcftools Tutorial
written 3.2 years ago by ▴ 140
11
votes
6
replies
1.4k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
20 days ago by Barry Digby ▴ 970
8
votes
0
replies
657
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
4 months ago by dariober 13k
2
votes
0
replies
522
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell Biology R Computational signalling
4 months ago by sinha.shriprakash ▴ 20
0
votes
0
replies
1.8k
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
4 months ago by Wayne ★ 1.1k
12
votes
4
replies
3.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Tutorial linux bioinformatics R
updated 5 months ago by • 0 • written 15 months ago by ▴ 120
19
votes
9
replies
33k
views
8 follow
Tutorial: Installing an updated R version (>=4.0) using conda
Tutorial error software R
updated 6 months ago by 36k • written 14 months ago by ★ 1.2k
1
vote
0
replies
915
views
Tutorial: Unsupervised clustering on gene expression data
clustering RNA-seq expression gene
8 weeks ago by Hamid Ghaedi ★ 2.5k
33
votes
6
replies
11k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 4 months ago by ▴ 10 • written 14 months ago by 8.2k
139
votes
67
replies
38k
views
17 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 7 months ago by ▴ 10 • written 4.5 years ago by 81k
122
votes
119
replies
22k
views
22 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
10 days ago by Kevin Blighe 81k
14
votes
1
reply
887
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 8 months ago by 13k • written 8 months ago by ▴ 200
192
votes
47
replies
65k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 3 months ago by • 0 • written 9.6 years ago by 19k
19
votes
1
reply
1.6k
views
Tutorial: Building Docker images
singularity container docker
7 months ago by ATpoint 60k
6
votes
2
replies
682
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
9 months ago by Kevin Blighe 81k
0
votes
0
replies
613
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
9 months ago by mo • 0
1
vote
0
replies
765
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
9 months ago by Kevin Blighe 81k
45
votes
2
replies
34k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa tutorial Tutorial
updated 10 months ago by • 0 • written 10.1 years ago by ▴ 540
85
votes
95
replies
27k
views
23 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 11 days ago by • 0 • written 3.7 years ago by 81k
69
votes
19
replies
8.7k
views
15 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
25 days ago by Hamid Ghaedi ★ 2.5k
0
votes
0
replies
491
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
11 months ago by Erin Haskell | ELIXIR ▴ 460
1
vote
0
replies
674
views
Tutorial: Slurm and parallelization
slurm
11 months ago by Juke34 ★ 6.9k
1
vote
0
replies
590
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
11 months ago by Pratik ▴ 770
12
votes
1
reply
1.2k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 11 months ago by ★ 13k • written 11 months ago by 81k
113
votes
66
replies
34k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump ENA Fastq Tutorial
10 months ago by ATpoint 60k
4
votes
0
replies
619
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
11 months ago by pbpanigrahi ▴ 410
0
votes
1
reply
476
views
Tutorial: Add Customized Filters in GDC
gdc
updated 11 months ago by 20k • written 11 months ago by ▴ 510
61
votes
26
replies
8.1k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 11 months ago by ▴ 180 • written 3.2 years ago by 15k
11
votes
20
replies
9.3k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
11 months ago by jared.andrews07 ★ 13k
4
votes
2
replies
1.6k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle 5.0 Tutorial
updated 12 months ago by 115k • written 2.9 years ago by ★ 9.0k
30
votes
13
replies
26k
views
9 follow
Tutorial: Using R in Conda
R Tutorial
updated 9 weeks ago by • 0 • written 22 months ago by ▴ 460
30
votes
8
replies
15k
views
10 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 3 months ago by • 0 • written 21 months ago by ▴ 140
98
votes
16
replies
27k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
16 days ago by Jean-Karim Heriche 25k
16
votes
1
reply
1.9k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 13 months ago by 51k • written 13 months ago by ★ 6.9k
31
votes
6
replies
6.0k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
8 months ago by Kevin Blighe 81k
75
votes
40
replies
25k
views
23 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 11 weeks ago by 36k • written 8.6 years ago by ★ 7.5k
75
votes
1
reply
49k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 8.9 years ago by 11k
8
votes
0
replies
1.4k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
13 months ago by rpolicastro 8.2k
233
votes
176
replies
77k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 9 weeks ago by 36k • written 6.8 years ago by ★ 4.5k
6
votes
0
replies
877
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
13 months ago by rpolicastro 8.2k
8
votes
1
reply
707
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
14 months ago by Kevin Blighe 81k
15
votes
9
replies
3.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 8 months ago by ★ 1.0k • written 20 months ago by 8.2k
12
votes
2
replies
794
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
13 months ago by rpolicastro 8.2k
349 results • Page 1 of 7
Recent Votes
Lasso regression and cross-validation on RNA seq dataset
Answer: Lasso regression and cross-validation on RNA seq dataset
A: Is it possible to run haplotypecaller in gnu parallel ?
Is it possible to run haplotypecaller in gnu parallel ?
A: Identifying De Novo Mutations from vcf files
Answer: Lasso regression and cross-validation on RNA seq dataset
A: How to combine multiple pheatmap figures and use common legend?
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Popular Question to mrashad ▴ 60
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Recent Replies
Comment: R: problem with running time-series analysis software: Mfuzz by Kevin Blighe 81k
Cross-posted: https://support.bioconductor.org/p/9144396/
Answer: Lasso regression and cross-validation on RNA seq dataset by Mensur Dlakic ★ 18k
It is not clear whether you have 192 datasets or 192 features in some undefined number of datasets, but either way cross validation is a sm…
Comment: SARS-CoV-2 lineages complete reference genomes by GenoMax 115k
I don't know if the following two resources are going to provide `reference` genomes. You may have to go to GSAID for that.
Answer: SARS-CoV-2 lineages complete reference genomes by GenoMax 115k
From EBI: https://www.covid19dataportal.org/sequences?crossReferencesOption=all ![EBI][1] [1]: /media/images/04dd9b11-77a8-4327-8…
Answer: Software to draw protein domains of proteins by cmdcolin ★ 2.1k
tools mentioned by other users are great, a couple more tools here https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag…
Answer: SARS-CoV-2 lineages complete reference genomes by GenoMax 115k
At [**NCBI SARS-CoV-2**][1] resource page. Be sure to switch to `Nucleotide` tab and then click on pango lineage search. ![Pango][2] …
Answer: comparisons between 2 ChIP-seq datasets by jared.andrews07 ★ 13k
Honestly, I'd just eyeball the tracks in IGV. It's usually pretty apparent. If you want more objective measures, you could look at total…
Comment: data correaltion by Jeremy ▴ 130
FYI the cor.test() function will display a p-value in addition to the correlation coefficient.
Comment: Inflation in Imputed data by desicasares@gmail.com ▴ 10
Thank you for your answer...the populations I am using are Spanish, North European and Italian individuals. In the case of the Italians t…
Comment: MAF in R by malgorzata.sobczak07 • 0
You're the best! Thanks! :)
Comment: Help with kallisto-bustools: how to interpret the inspect.json output file by dsull ★ 3.0k
Correct, which is why you should load your output into R or python and filter your cells (i.e. do the "knee plot"). See the kallisto | bust…
Answer: MAF in R by Ram 36k
You can use `HardyWeinberg::maf` to calculate MAF from a vector of frequencies. You can create this vector of HOM/HET/HOM-ALT frequencies u…
Comment: MAF in R by malgorzata.sobczak07 • 0
Yeah, sorry :)
Comment: MAF in R by Ram 36k
Your code won't work. You'll need to quote the allele strings
Comment: The minor allele frequency by Negatyvna • 0
Yes, I would like to do the second option
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