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76
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2
replies
50k
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Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 9.0 years ago by 11k
12
votes
5
replies
9.6k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr gene RNA-Seq R Tutorial
updated 7 weeks ago by 81k • written 4.6 years ago by ▴ 640
1
vote
0
replies
435
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
TCGA Counts v32.0 Biolinks GDC STAR
10 weeks ago by dare_devil ★ 1.6k
29
votes
3
replies
6.5k
views
7 follow
Tutorial: Methylation Analysis Tutorial in R_part1
Tutorial cancer methylation R
updated 11 weeks ago by 117k • written 21 months ago by ★ 2.5k
1
vote
2
replies
473
views
Tutorial: Running fastq_screen on your data
fastqscreen
3 months ago by rohitsatyam102 ▴ 510
7
votes
12
replies
979
views
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 4 months ago by ▴ 640 • written 4 months ago by ▴ 30
70
votes
14
replies
12k
views
15 follow
Tutorial: List Of Bioinformatics Books
bioinformatics tutorial books Tutorial
updated 4 months ago by ▴ 30 • written 9.1 years ago by 9.3k
23
votes
13
replies
2.8k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 5 months ago by ▴ 880 • written 8 months ago by 93k
3
votes
13
replies
6.7k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf merge bcftools Tutorial
written 3.4 years ago by ▴ 140
12
votes
9
replies
1.9k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 14 days ago by ▴ 30 • written 6 months ago by ▴ 980
9
votes
0
replies
824
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
5 months ago by dariober 13k
2
votes
0
replies
599
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell Biology R Computational signalling
5 months ago by sinha.shriprakash ▴ 20
0
votes
0
replies
2.7k
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
5 months ago by Wayne ★ 1.2k
12
votes
4
replies
3.6k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Tutorial linux bioinformatics R
updated 7 months ago by • 0 • written 16 months ago by ▴ 120
21
votes
10
replies
37k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
Tutorial error software R
updated 4 weeks ago by • 0 • written 15 months ago by ★ 1.2k
1
vote
0
replies
1.1k
views
Tutorial: Unsupervised clustering on gene expression data
clustering RNA-seq expression gene
3 months ago by Hamid Ghaedi ★ 2.5k
35
votes
6
replies
12k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 5 months ago by ▴ 10 • written 15 months ago by 8.8k
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 8 months ago by ▴ 10 • written 4.6 years ago by 81k
122
votes
119
replies
23k
views
22 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
6 weeks ago by Kevin Blighe 81k
14
votes
1
reply
944
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 9 months ago by 13k • written 9 months ago by ▴ 200
192
votes
47
replies
66k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 4 months ago by ▴ 10 • written 9.7 years ago by 19k
20
votes
1
reply
1.7k
views
Tutorial: Building Docker images
singularity container docker
9 months ago by ATpoint 62k
6
votes
2
replies
718
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
10 months ago by Kevin Blighe 81k
0
votes
0
replies
646
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
10 months ago by mo • 0
1
vote
0
replies
853
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
10 months ago by Kevin Blighe 81k
45
votes
2
replies
34k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa tutorial Tutorial
updated 11 months ago by • 0 • written 10.2 years ago by ▴ 540
86
votes
95
replies
28k
views
23 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 6 weeks ago by • 0 • written 3.8 years ago by 81k
70
votes
19
replies
9.3k
views
15 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
8 weeks ago by Hamid Ghaedi ★ 2.5k
0
votes
0
replies
514
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
12 months ago by Erin Haskell | ELIXIR ▴ 460
1
vote
0
replies
701
views
Tutorial: Slurm and parallelization
slurm
12 months ago by Juke34 ★ 7.1k
1
vote
0
replies
615
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
12 months ago by Pratik ▴ 770
12
votes
1
reply
1.3k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 12 months ago by ★ 13k • written 12 months ago by 81k
113
votes
66
replies
35k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump ENA Fastq Tutorial
11 months ago by ATpoint 62k
4
votes
0
replies
641
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
12 months ago by pbpanigrahi ▴ 410
0
votes
1
reply
504
views
Tutorial: Add Customized Filters in GDC
gdc
updated 13 months ago by 20k • written 13 months ago by ▴ 540
61
votes
26
replies
8.4k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 13 months ago by ▴ 180 • written 3.3 years ago by 15k
11
votes
20
replies
9.5k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
13 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 13 months ago by 117k • written 3.0 years ago by ★ 9.1k
32
votes
13
replies
30k
views
9 follow
Tutorial: Using R in Conda
R Tutorial
updated 3 months ago by • 0 • written 23 months ago by ▴ 510
31
votes
9
replies
16k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 4 weeks ago by • 0 • written 22 months ago by ▴ 140
98
votes
16
replies
27k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
7 weeks ago by Jean-Karim Heriche 25k
18
votes
1
reply
2.1k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 14 months ago by 51k • written 14 months ago by ★ 7.1k
31
votes
6
replies
6.3k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
10 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 3 months ago by 36k • written 8.7 years ago by ★ 7.5k
8
votes
0
replies
1.5k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
15 months ago by rpolicastro 8.8k
233
votes
176
replies
78k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 3 months ago by 36k • written 6.9 years ago by ★ 4.5k
6
votes
0
replies
945
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
15 months ago by rpolicastro 8.8k
8
votes
1
reply
742
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
15 months ago by Kevin Blighe 81k
15
votes
9
replies
3.2k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 9 months ago by ★ 1.1k • written 22 months ago by 8.8k
12
votes
2
replies
816
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
15 months ago by rpolicastro 8.8k
348 results • Page 1 of 7
Recent Votes
Answer: ESTIMATE tumor purity
C: Run PHI-BLAST in BLAST+ standalone
Answer: Junior bioinformatician in italy
Junior bioinformatician in italy
A: Thoughts on switching from Biology to Bioinformatics
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
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Recent Awards • All
Scholar to JACKY ▴ 10
Scholar to Marco Pannone ▴ 290
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Popular Question to el97004 ▴ 50
Scholar to Pierre Lindenbaum 146k
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Recent Replies
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK by chrchang523 9.3k
If 1kgtot.bim contains doubled IDs (e.g. "HG00096 HG00096", you need to provide a doubled ID to `--indv`. The log file shows that your scr…
Answer: ESTIMATE tumor purity by JACKY ▴ 10
Just in case anyone faces this problem in the future, here is the link for the updated `estimate package` on github: https://github.com/…
Answer: Exctract unmapped reads from BLAST by GenoMax 117k
> Is there a way to tell blast to output the unmapped reads into a > separate file? No there is not. You will need to use `-outfmt 7` whe…
Comment: Resfams Database usage by Neel ▴ 10
Hi, i have annotated genome by prokka and o want to search amr agaisnt resfams could you please tell me how to do it steps by steps.
Comment: Exctract unmapped reads from BLAST by Pierre Lindenbaum 146k
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join extract the names of your queries, s…
Comment: Exctract unmapped reads from BLAST by Pilar • 0
Thanks for answering :), sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?
Comment: Exctract unmapped reads from BLAST by Pierre Lindenbaum 146k
have a look at `comm` or `join`.
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK by pifferdavide ▴ 100
Sorry I forgot to mention I used it in this loop, which worked with another plink file, but not with this 1KG file. for popfile in $(l…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK by chrchang523 9.3k
`--indv` takes a single ID, not a filename. So `--indv IDlist.txt` shouldn't work.
Answer: Quast Ouput by Ying • 0
The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw nu…
Answer: SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM by Mensur Dlakic ★ 19k
Not sure why: 1) you are splitting reads; 2) you are fixing reads when they seem fine. I suggest something like this instead after `prefetc…
Comment: Quick way to get a field such as QNAME from the last read in a bam file? by kalavattam ▴ 70
Thank you. Do you know of any strategies for non-coordinated-sorted bam files?
Comment: analyzing a single cell and searching for a specific gene using single cell data by jared.andrews07 ★ 13k
@rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer al…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK by pifferdavide ▴ 100
I was able to run the --indv command successfully on a file with a bed file by simply listing the IDs in single column. However, with anoth…
Answer: Get nucleotide sequence of assembled RNA transcripts by tomas4482 ▴ 140
1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing. 2. subset to interested region -> extract chi…
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