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12
votes
5
replies
9.4k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr gene RNA-Seq R Tutorial
updated 15 days ago by 81k • written 4.5 years ago by ▴ 610
0
votes
0
replies
284
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
TCGA Counts v32.0 Biolinks GDC STAR
6 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
349
views
Tutorial: Running fastq_screen on your data
fastqscreen
9 weeks ago by rohitsatyam102 ▴ 460
7
votes
12
replies
879
views
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 12 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
2.5k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 4 months ago by ▴ 880 • 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 3.3 years ago by ▴ 140
11
votes
6
replies
1.5k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
23 days ago by Barry Digby ▴ 970
8
votes
0
replies
671
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
528
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
1.9k
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
34k
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
924
views
Tutorial: Unsupervised clustering on gene expression data
clustering RNA-seq expression gene
9 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
14 days ago by Kevin Blighe 81k
14
votes
1
reply
893
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 9.7 years ago by 19k
19
votes
1
reply
1.6k
views
Tutorial: Building Docker images
singularity container docker
8 months ago by ATpoint 61k
6
votes
2
replies
685
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
616
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
774
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 14 days ago by • 0 • written 3.7 years ago by 81k
69
votes
19
replies
8.8k
views
15 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
29 days ago by Hamid Ghaedi ★ 2.5k
0
votes
0
replies
494
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
680
views
Tutorial: Slurm and parallelization
slurm
11 months ago by Juke34 ★ 6.9k
1
vote
0
replies
593
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 61k
4
votes
0
replies
622
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
11 months ago by pbpanigrahi ▴ 410
0
votes
1
reply
479
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
12 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
19 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
9 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
14 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
883
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
14 months ago by rpolicastro 8.2k
8
votes
1
reply
714
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
796
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
14 months ago by rpolicastro 8.2k
349 results • Page 1 of 7
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Answer: Retrieve All Genes Associated With A Go Term
Comment: awk command help
A: Table browser +/- 2Kb of TSS export
C: Pca From Vcf Files
A: EdgeR analysis with CPM normalzed counts
Comment: PC build for Nanopore data analysis
Comment: PC build for Nanopore data analysis
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Recent Replies
Answer: Biopython intron-exon boundary nucleotide frequencies by Joe 20k
Eukaryote genomics is not a area of expertise for me so apologies if I miss some subtlety with the exons/introns here, but if the tasks is …
Comment: BED file from GSEA gene set by ATpoint 61k
What exactly is the question? Do you need code to make a BED file, and if so based on what? Gene symbols, coordinates of peaks? Please add …
Comment: Strange Trimmomatic behavior by lieven.sterck 13k
can you first confirm it is GBS data we're talking about here?
Comment: arrange samples in same order in rows and column in R by Bioinfonext ▴ 380
This also shows error, Is there any way in R to arrange samples in same rows/column? fit <- lmFit(t(mval), var) Error in lmFit(t(mval),…
Comment: PC build for Nanopore data analysis by Jean-Karim Heriche 25k
I assumed that this was already covered because of the mention of > a pipeline for the data that is subsequently generated
Answer: PC build for Nanopore data analysis by GenoMax 115k
I assume you are referring to MinION sequencing since other larger ONT sequencers are supplied with built in compute for doing some of the …
Comment: PC build for Nanopore data analysis by GenoMax 115k
ONT basecallers are [**performant only with GPU**][1]'s. [1]: https://hackmd.io/@Miles/B1U-cOMyu#GPUs-and-Guppy-base-calling
Comment: bcftools stats: definition of indel type by WouterDeCoster 46k
But it requires that there is a match between a part of the REF allele and a part of the ALT allele (https://github.com/samtools/htslib/blo…
Comment: bcftools stats: definition of indel type by Pierre Lindenbaum 145k
// i and j are the position in the alt and ref string if ( a[i]!=END_OF_STRING && r[j]==END_OF-STRING ) { …
Comment: bcftools stats: definition of indel type by Pierre Lindenbaum 145k
so looking quickly an indel is when this is not a symbolic allele (<BND>) and the length of REF and the current ALT are not the same.
Comment: bcftools stats: definition of indel type by WouterDeCoster 46k
Yes, but I cannot figure out in which cases the INDEL type is assigned: ``` if ( *a && !*r ) { if ( *a==']' || *a=='[' ) { …
Answer: MG RAST for Eukaryota by young_bioinformatician ▴ 170
Hi Tom, Yes, you can go with the predicted proteins for the annotation/downstream analysis.
Comment: bcftools stats: definition of indel type by Pierre Lindenbaum 145k
if the type hasn't been already defined, the type is set as an array of bytes using `OR` and this function: https://github.com/samtools/hts…
Comment: arrange samples in same order in rows and column in R by Kevin Blighe 81k
You probably just need: fit <- lmFit(t(mval), var) In your model, you are also attempting to adjust for a lot of covariates- is that…
Comment: arrange samples in same order in rows and column in R by Bioinfonext ▴ 380
Thank Basti, I already did this, could you please above posted full code? Many thanks,
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