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87
votes
2
replies
59k
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6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 14 months ago by 43k • written 10.8 years ago by 11k
16
votes
5
replies
13k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 13 months ago by 43k • written 6.4 years ago by ▴ 800
3
votes
2
replies
2.8k
views
Tutorial: Running fastq_screen on your data
fastqscreen
2.1 years ago by rohitsatyam102 ▴ 840
9
votes
14
replies
3.7k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 18 months ago by ▴ 10 • written 2.2 years ago by ▴ 40
76
votes
14
replies
16k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
35
votes
13
replies
14k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 2.2 years ago by ★ 1.4k • written 2.5 years ago by 100k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 10 months ago by 43k • written 5.2 years ago by ▴ 170
16
votes
9
replies
7.0k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 22 months ago by ▴ 70 • written 2.4 years ago by ★ 1.3k
0
votes
0
replies
11k
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
2.3 years ago by Wayne ★ 2.0k
12
votes
4
replies
5.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 14 months ago by 43k • written 3.2 years ago by ▴ 130
30
votes
10
replies
81k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 13 months ago by 43k • written 3.1 years ago by ★ 1.6k
44
votes
6
replies
24k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 2.3 years ago by ▴ 40 • written 3.1 years ago by 13k
149
votes
70
replies
50k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 7 months ago by ▴ 260 • written 6.4 years ago by 87k
15
votes
2
replies
2.1k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 18 months ago by ▴ 830 • written 2.6 years ago by ▴ 300
196
votes
44
replies
71k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 15 months ago by 43k • written 11.6 years ago by 20k
6
votes
2
replies
1.6k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.7 years ago by Kevin Blighe 87k
0
votes
0
replies
1.2k
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
2.7 years ago by mo • 0
3
votes
1
reply
3.4k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
updated 10 weeks ago by ▴ 120 • written 2.7 years ago by 87k
45
votes
2
replies
37k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 14 months ago by 43k • written 12.0 years ago by ▴ 540
98
votes
106
replies
46k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 15 days ago by ▴ 20 • written 5.6 years ago by 87k
0
votes
0
replies
1.1k
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
2.9 years ago by Erin Haskell | ELIXIR ▴ 470
1
vote
0
replies
1.3k
views
Tutorial: Slurm and parallelization
slurm
2.9 years ago by Juke34 8.5k
1
vote
0
replies
1.3k
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
2.9 years ago by Pratik ★ 1.0k
14
votes
1
reply
3.1k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.9 years ago by ★ 16k • written 2.9 years ago by 87k
117
votes
66
replies
46k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 13 months ago by 43k • written 5.8 years ago by 81k
4
votes
0
replies
1.2k
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
2.9 years ago by pbpanigrahi ▴ 420
0
votes
1
reply
1.1k
views
Tutorial: Add Customized Filters in GDC
gdc
updated 2.9 years ago by 21k • written 2.9 years ago by ★ 1.2k
12
votes
20
replies
14k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 13 months ago by 43k • written 4.9 years ago by ★ 16k
4
votes
2
replies
2.5k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 13 months ago by 43k • written 4.9 years ago by ★ 9.4k
54
votes
14
replies
91k
views
10 follow
Tutorial: Using R in Conda
R
updated 13 months ago by 43k • written 3.8 years ago by ▴ 840
99
votes
16
replies
33k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 13 months ago by 43k • written 7.7 years ago by 27k
22
votes
2
replies
5.8k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 19 months ago by ▴ 40 • written 3.0 years ago by 8.5k
32
votes
6
replies
12k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 13 months ago by 43k • written 3.9 years ago by 87k
8
votes
0
replies
2.7k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
3.1 years ago by rpolicastro 13k
239
votes
176
replies
95k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 11 months ago by 43k • written 8.7 years ago by ★ 4.7k
6
votes
0
replies
2.3k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
3.1 years ago by rpolicastro 13k
8
votes
1
reply
1.4k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 13 months ago by 43k • written 3.1 years ago by 87k
22
votes
10
replies
7.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 13 months ago by 43k • written 3.6 years ago by 13k
12
votes
2
replies
1.3k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 13 months ago by 43k • written 3.1 years ago by 13k
149
votes
35
replies
62k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 14 months ago by 43k • written 11.4 years ago by ★ 1.6k
16
votes
7
replies
16k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 13 months ago by 43k • written 4.9 years ago by ▴ 310
298
votes
33
replies
108k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 13 months ago by 43k • written 10.5 years ago by 20k
6
votes
2
replies
5.0k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
4 months ago by GenoMax 141k
11
votes
0
replies
6.8k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 13 months ago by 43k • written 3.3 years ago by 141k
10
votes
0
replies
4.9k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 13 months ago by 43k • written 3.3 years ago by 141k
11
votes
1
reply
2.6k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 13 months ago by 43k • written 3.3 years ago by ★ 27k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 13 months ago by 43k • written 10.0 years ago by ★ 1.9k
0
votes
1
reply
3.0k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 13 months ago by 43k • written 5.7 years ago by ▴ 320
77
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.5 years ago by 43k • written 9.9 years ago by 19k
6
votes
10
replies
5.2k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 13 months ago by 43k • written 6.2 years ago by ▴ 370
410 results • Page 3 of 9
Recent Votes
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
RNA-seq power estimation using ssizeRNA program
Answer: WGCNA preservation analysis
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
ISCN annotation for SV/CN VCF files
Comment: How to convert plink files to Hapmap Format
Am I crazy, or are most published RNA-seq studies vastly underpowered?
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Popular Question to AdviceSeeker • 0
Great Question to Ann ★ 2.4k
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Recent Replies
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
You simply need to make a list of barcodes one on each line: https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-wh…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by GenoMax 141k
> What specifications and operating system would be ideal for my case? For choice of OS: Linux to access the large pool of open source sof…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Ok. First update your phenotypes because in the 6th column all the values are -9 meaning missing, and then run `--assoc`. You can do the fo…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by i.sudbery 19k
You'll probably get away with using one of the other analysis pipelines, like Alevin-fry with much less than 128GB of RAM. Workstations can…
Comment: Difference between samtools "-f 9" and "-f 11" by Dylan • 0
> (which is weird, if it's in proper pair, read and its mate should be both mapped) So that was my thought as well, I think the code you l…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by Ram 43k
> several single cell samples At the same time? You need a server, not a PC. Google around (and search the site as well with keyword "conf…
Answer: Difference between samtools "-f 9" and "-f 11" by Pierre Lindenbaum 161k
9: read must be paired AND mate must be unmapped 11: read must be paired AND mapped in proper pair AND mate must be unmapped (which is w…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
the data is binary and associated with a disease but we're studying only the cases and there are other phenotypes of severity
Comment: Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Ser by atowns21 • 0
could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or do you have to re-format the…
Comment: How to trim transcripts using information from NCBI contamination screen report by GenoMax 141k
> I didn't do a good job with Trimmomatic for some reason so I have to do some trimming of my transcripts. If you had extraneous sequence…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Please answer my above question. What type of data is it, binary (cases and controls) or quantitative? You need to update Phenotype info in…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
This is how my .fam file looks like ![enter image description here][1] [1]: /media/images/caccd97c-3606-48d2-aa32-423a9882 And I run …
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
Answer: Redirection of Duplicate PMIDs by GenoMax 141k
> linked to a list of grants Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this w…
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