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340 results • Page 1 of 7
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6
votes
1
reply
123
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 2 days ago by 12k • written 2 days ago by ▴ 100
188
votes
47
replies
63k
views
32 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 14 days ago by • 0 • written 9.0 years ago by 19k
18
votes
2
replies
693
views
Tutorial: Building Docker images
singularity container docker
23 days ago by ATpoint 54k
6
votes
2
replies
277
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
5 weeks ago by Kevin Blighe 77k
0
votes
0
replies
210
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
6 weeks ago by mo • 0
0
votes
0
replies
168
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
7 weeks ago by Kevin Blighe 77k
44
votes
2
replies
32k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa tutorial Tutorial
updated 9 weeks ago by • 0 • written 9.5 years ago by ▴ 530
78
votes
92
replies
20k
views
21 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 9 days ago by ▴ 40 • written 3.1 years ago by 77k
56
votes
17
replies
4.9k
views
13 follow
Tutorial: Gene Set Enrichment Analysis
RNA-Seq GSEA enrichment microarray Tutorial
20 days ago by Hamid Ghaedi ★ 1.7k
0
votes
0
replies
206
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
3 months ago by Erin Haskell | ELIXIR ▴ 460
1
vote
0
replies
275
views
Tutorial: Slurm and parallelization
slurm
3 months ago by Juke34 ★ 6.3k
1
vote
0
replies
270
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
3 months ago by Pratik Mehta ▴ 580
9
votes
1
reply
536
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 3 months ago by ★ 11k • written 3 months ago by 77k
110
votes
66
replies
28k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump ENA Fastq Tutorial
10 weeks ago by ATpoint 54k
4
votes
0
replies
276
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
3 months ago by pbpanigrahi ▴ 410
0
votes
1
reply
199
views
Tutorial: Add Customized Filters in GDC
gdc
updated 3 months ago by 17k • written 3 months ago by ▴ 430
56
votes
26
replies
5.8k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 3 months ago by ▴ 180 • written 2.6 years ago by 14k
22
votes
1
reply
4.1k
views
Tutorial: Methylation Analysis Tutorial in R_part1
Tutorial cancer methylation R
updated 3 months ago by ▴ 30 • written 11 months ago by ★ 1.7k
11
votes
20
replies
7.0k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
3 months ago by jared.andrews07 ★ 11k
4
votes
2
replies
1.1k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle 5.0 Tutorial
updated 4 months ago by 106k • written 2.3 years ago by ★ 8.8k
14
votes
8
replies
9.0k
views
7 follow
Tutorial: Installing an updated R version (>=4.0) using conda
R software error Tutorial
updated 12 weeks ago by • 0 • written 6 months ago by ★ 1.1k
24
votes
11
replies
9.9k
views
7 follow
Tutorial: Using R in Conda
R Tutorial
updated 4 months ago by ★ 3.0k • written 14 months ago by ▴ 350
21
votes
6
replies
7.7k
views
8 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 7 days ago by • 0 • written 13 months ago by ▴ 120
90
votes
16
replies
24k
views
18 follow
Tutorial: Heatmaps in R
heatmap R Tutorial
updated 4 months ago by • 0 • written 5.1 years ago by 25k
13
votes
1
reply
658
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 5 months ago by 49k • written 5 months ago by ★ 6.3k
24
votes
6
replies
3.7k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
26 days ago by Kevin Blighe 77k
68
votes
38
replies
22k
views
22 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq bioconductor fpkm Forum Tutorial
updated 5 months ago by • 0 • written 7.9 years ago by ★ 7.4k
71
votes
1
reply
46k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 8.2 years ago by 11k
6
votes
0
replies
531
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
5 months ago by rpolicastro 5.9k
231
votes
175
replies
71k
views
72 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 6 months ago by 34k • written 6.1 years ago by ★ 4.5k
16
votes
0
replies
3.3k
views
Tutorial: Greatly speed up conda by using mamba
software
6 months ago by rpolicastro 5.9k
6
votes
0
replies
371
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
5 months ago by rpolicastro 5.9k
7
votes
1
reply
363
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
6 months ago by Kevin Blighe 77k
14
votes
9
replies
1.8k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 10 days ago by ▴ 940 • written 12 months ago by 5.9k
12
votes
2
replies
464
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
5 months ago by rpolicastro 5.9k
145
votes
34
replies
52k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 8 days ago by 34k • written 8.8 years ago by ★ 1.6k
7
votes
2
replies
1.7k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
R linux bioinformatics Tutorial
updated 6 months ago by • 0 • written 7 months ago by ▴ 70
14
votes
2
replies
1.3k
views
Tutorial: Methylation Analysis Tutorial in R_part2
methylation RNA-Seq R cancer Tutorial
6 months ago by Hamid Ghaedi ★ 1.7k
4
votes
0
replies
846
views
Tutorial: Building mosdepth on macOS
mosdepth nim Tutorial
5 months ago by ATpoint 54k
5
votes
6
replies
558
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 28 days ago by 17k • written 6 months ago by ▴ 130
73
votes
32
replies
11k
views
17 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 6 months ago by ▴ 10 • written 3.3 years ago by ★ 1.1k
11
votes
7
replies
6.8k
views
Tutorial: Integrating VDJ sequencing data with Seurat
Seurat clonotyping VDJ sc-RNAseq Tutorial
updated 7 months ago by 7.5k • written 2.3 years ago by ▴ 270
238
votes
32
replies
72k
views
22 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 7 months ago by ▴ 20 • written 7.9 years ago by 19k
4
votes
0
replies
2.0k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap Tutorial
8 months ago by GenoMax 106k
7
votes
0
replies
1.7k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap Tutorial
8 months ago by GenoMax 106k
8
votes
0
replies
996
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap Tutorial
8 months ago by GenoMax 106k
9
votes
1
reply
906
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq Tutorial
updated 8 months ago by 54k • written 8 months ago by ★ 13k
34
votes
9
replies
9.4k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
Tutorial flow-cytometry single-cell
updated 4.8 years ago by ▴ 30 • written 7.4 years ago by ★ 1.9k
0
votes
1
reply
1.8k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
taxonomy python biosql Tutorial
updated 9 months ago by • 0 • written 3.1 years ago by ▴ 270
73
votes
13
replies
12k
views
12 follow
Tutorial: Exploring cancer mutation data portals
Cancer Data Portal Mutation TCGA ICGC Tutorial
9 months ago by Malachi Griffith 19k
340 results • Page 1 of 7
Recent Votes
Comment: Exclude pseudogenes and lncRNA's from DE-analysis?
how to remove multiallelic from VCF
Answer: Exclude pseudogenes and lncRNA's from DE-analysis?
Answer: Exclude pseudogenes and lncRNA's from DE-analysis?
Comment: Did not take note of my indices (barcodes); is my library salvageable?
Comment: align_and_estimate_abundance error Trinty
Answer: Proper way(s) to perform enrichment analysis in R
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Recent Replies
Comment: Exclude pseudogenes and lncRNA's from DE-analysis? by Barista ▴ 10
That makes perfect sense, thank you!
Comment: Bioinformatics tutoring by ATpoint 54k
Again, very open-ended statement. "it won't run", what does that mean? Here is an end-to-end workflow for Affy arrays, maybe that helps: ht…
Comment: Beginner problems: Aligning "genomes" that come in contigs by 5heikki 9.9k
What do you mean when you say that you want to compare the genomes to each other via whole genome alignment? Do you really want to look at …
Comment: Exclude pseudogenes and lncRNA's from DE-analysis? by ATpoint 54k
I think it is good that they contribute, more genes make everything more reliable (norm/disp). They were sequenced as part of the library s…
Comment: NGS raw data manipulation using Linux/Unix by 5heikki 9.9k
If you go from: @SEQ_ID GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT + !''*((((***+))%%%++)(%%%%).1***-+*'…
Comment: Bioinformatics tutoring by Michael Dondrup 49k
I suggest to work your way through step by step, then if something fails: google the error message. If that doesn't lead you anywhere, post…
Comment: PSMC Illegal division by zero by gubrins ▴ 90
Can you update the code for performing bootstrap with PSMC? I'm having a problem in this line: seq 100 | xargs -i echo psmc -N25 -t15 …
Comment: Bioinformatics tutoring by bioinformatics • 0
Thankyou for your response. Yes I have read through it but I only understand parts of it. e.g. So I can only filter out the lowly express…
Comment: Exclude pseudogenes and lncRNA's from DE-analysis? by Barista ▴ 10
Hi ATpoint, Thanks for you reply, I really find it an interesting topic, because I can imagine that when the functions of those genes are…
Answer: Can anyone suggest the good tool for identification of deregulated pathway by Mu by i.sudbery 13k
Try MOFA: https://biofam.github.io/MOFA2/ It is a bit like PCA, but will use a variety of different 'omics data types to find the import…
Comment: scvelo latent time vs pseudotime by ATpoint 54k
To my knowledge both are the inferred developmental trajectories, with early time being more undifferentiated- and late time being more dif…
Comment: align_and_estimate_abundance error Trinty by Princy ▴ 20
yes, it's an error because the output file is empty.
Comment: Did not take note of my indices (barcodes); is my library salvageable? by ATpoint 54k
After all you can also first amplify an aliquot per library (normal amplification PCR), put on gel, excise a precise band and then send tha…
Answer: Exclude pseudogenes and lncRNA's from DE-analysis? by ATpoint 54k
If you are not interested in them then I would exclude them prior to FDR adjustment, that would be the `results` step in `DESeq2` or the `t…
Comment: bcftools by ATpoint 54k
If you really want to compile then download the `tar.bz2` release package from https://github.com/samtools/bcftools/releases which contains…
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