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348 results • Page 1 of 7
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76
votes
2
replies
50k
views
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 6 weeks ago by 81k • written 4.6 years ago by ▴ 640
1
vote
0
replies
431
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 20 months ago by ★ 2.5k
1
vote
2
replies
470
views
Tutorial: Running fastq_screen on your data
fastqscreen
3 months ago by rohitsatyam102 ▴ 510
7
votes
12
replies
978
views
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 3 months ago by ▴ 640 • written 3 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
2.7k
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 3.3 years ago by ▴ 140
12
votes
9
replies
1.9k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 13 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
593
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 6 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 29 days 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
717
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
644
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
851
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
513
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
700
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 12 months ago by 20k • written 12 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 12 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 29 days 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
939
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
741
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
VQSR bias against rare variants
Answer: pymol for superimpose by python script
Comment: aligner for CORRECTED pacbio long reads
How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
A: How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
Comment: How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
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Popular Question to predeus ★ 1.8k
Scholar to rpolicastro 8.8k
Scholar to GenoMax 117k
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Recent Replies
Comment: analyzing a single cell and searching for a specific gene using single cell data by Bioinfo • 0
@rpolicastro yes they do have the h5ad data but I cannot figure how to make a use out of it. It seems they just cluster things and that is …
Comment: pymol for superimpose by python script by iamsmor • 0
Thank you so much, you really wonderful person, spend your time for long detailed explaination.
Answer: Problem using FastML for ancestral sequence reconstruction by Mensur Dlakic ★ 19k
It does not seem that you understand the meaning of this error message: > sh: 1: cannot create outdir/fastml.std: Directory nonexistent …
Comment: aligner for CORRECTED pacbio long reads by gconcepcion ▴ 280
This is a very old and outdated link, what is it exactly that you are trying to do? Align PacBio HiFi reads to a reference? Try minimap…
Comment: How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go? by sunnykevin97 ▴ 760
You have to use the nucleotide (CDS) alignment file as input.
Comment: What Is Ad (Allelic Depth) In 1000Genomes Vcf? by Maryam • 0
Hello, This post is so helpful. My question is according to quality scoring of variants, the good AD threshold should be >8. Then how…
Comment: Incomplete alignment EMBOSS needleall by lieven.sterck 14k
not sure if it takes fastq as input (though yes, there example on their site is named .fastq , but when you look at that file it is a fasta…
Comment: Extract sequence from Fasta using header by GenoMax 117k
@princy: You have asked many questions on biostars over the last few months but appear not to have validated any of them. Accepting answers…
Answer: Extract sequence from Fasta using header by lieven.sterck 14k
`seqkit` will be able to do this. (subprogram `seq` ) (alternative, if you have a blastdb of that fasta file, you can also get them by u…
Answer: Extract sequence from Fasta using header by GenoMax 117k
See: https://www.biostars.org/p/434016/#434038
Comment: Best pipeline for RNAseq assembly and analysis (or help with stringtie assembly) by Katherine • 0
I thought that the file I used was the most up to date. Here is the header of the file: gff-version 3 !gff-spec-version 1.21 !processor…
Comment: analyzing a single cell and searching for a specific gene using single cell data by rpolicastro 8.8k
They provide an h5ad file, which may contain the already processed data, plus associated cell and feature metadata. If so, you should load …
Answer: Extract header from fasta file by cpad0112 20k
$ awk -F "_|:" -v OFS="_" '/^>/{print ">"$2,$3,$4,$5,$6};!/>/' test.fa >TRINITY_DN74698_c0_g1_i1 MRIRSVVFTLRPRAKWMAPSSGMRL…
Answer: analyzing a single cell and searching for a specific gene using single cell data by jared.andrews07 ★ 13k
I'd recommend you read what goes into a single cell analysis. The [Orchestrating Single Cell Analysis](http://bioconductor.org/books/releas…
Answer: Extract header from fasta file by rpolicastro 8.8k
A [seqkit](https://bioinf.shenwei.me/seqkit/) answer. You may need to tweak the regex depending on the variability in the naming scheme. `…
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