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73
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18
replies
65k
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12 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools bcftools htslib Tutorial
updated 2 days ago by 37k • written 4.4 years ago by ▴ 500
72
votes
60
replies
22k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
updated 6 days ago by • 0 • written 5.2 years ago by 84k
82
votes
28
replies
27k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR BioConductor R Graphics Tutorial
updated 4 weeks ago by 123k • written 6.7 years ago by 20k
0
votes
1
reply
315
views
Tutorial: Package is not available (for R version XXX)？ Manually download and install R packages
installation package R
updated 6 weeks ago by 11k • written 6 weeks ago by ▴ 30
11
votes
31
replies
4.3k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
gene geneset abinitio Tutorial genome
6 weeks ago by Juke34 7.4k
1
vote
2
replies
302
views
Tutorial: ViennaRNA package installation in Windows
install mfold viennarna rna windows
updated 10 weeks ago by 9.4k • written 11 weeks ago by ▴ 20
0
votes
0
replies
183
views
Tutorial: Making LDA Score plot
LDA metagenomics
10 weeks ago by rohitsatyam102 ▴ 680
128
votes
122
replies
26k
views
23 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 3 months ago by • 0 • written 4.1 years ago by 84k
9
votes
7
replies
4.4k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 3 months ago by • 0 • written 21 months ago by ▴ 190
11
votes
1
reply
1.7k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 3 months ago by ★ 1.7k • written 11 months ago by 13k
13
votes
8
replies
1.9k
views
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
20 days ago by ATpoint 66k
79
votes
21
replies
12k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
updated 3 months ago by • 0 • written 2.1 years ago by 2.8k
3
votes
0
replies
313
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
3 months ago by Kevin Blighe 84k
10
votes
5
replies
2.3k
views
6 follow
Tutorial: The Machine Learning Technology for The Beginners
machine learning Tutorial
written 4.5 years ago by ▴ 60
24
votes
0
replies
2.3k
views
Tutorial: Building Docker images
singularity docker container
4 months ago by ATpoint 66k
1
vote
1
reply
6.0k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 4 months ago by ★ 2.5k • written 4 months ago by ▴ 10
83
votes
34
replies
14k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 4 months ago by 37k • written 4.5 years ago by ★ 1.3k
76
votes
2
replies
52k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 9.4 years ago by 11k
15
votes
5
replies
10k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr gene RNA-Seq R Tutorial
updated 7 months ago by 84k • written 5.0 years ago by ▴ 740
1
vote
0
replies
942
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
TCGA Counts v32.0 Biolinks GDC STAR
8 months ago by dare_devil ★ 1.7k
37
votes
8
replies
8.1k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer Tutorial R methylation
updated 6 days ago by ★ 1.1k • written 2.2 years ago by 2.8k
3
votes
2
replies
933
views
Tutorial: Running fastq_screen on your data
fastqscreen
8 months ago by rohitsatyam102 ▴ 680
7
votes
14
replies
1.6k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 5 weeks ago by • 0 • written 9 months ago by ▴ 30
74
votes
14
replies
13k
views
15 follow
Tutorial: List Of Bioinformatics Books
bioinformatics tutorial books Tutorial
updated 12 weeks ago by 37k • written 9.6 years ago by 9.4k
23
votes
13
replies
4.9k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 10 months ago by ★ 1.1k • written 13 months ago by 96k
3
votes
13
replies
8.4k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf merge bcftools Tutorial
written 3.8 years ago by ▴ 140
12
votes
9
replies
3.1k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 5 months ago by ▴ 40 • written 12 months ago by ★ 1.1k
2
votes
0
replies
823
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell Biology R Computational signalling
11 months ago by sinha.shriprakash ▴ 20
0
votes
0
replies
6.0k
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
11 months ago by Wayne ★ 1.5k
12
votes
4
replies
4.1k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Tutorial linux bioinformatics R
updated 12 months ago by • 0 • written 22 months ago by ▴ 120
24
votes
10
replies
52k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
Tutorial error software R
updated 6 months ago by • 0 • written 20 months ago by ★ 1.3k
5
votes
2
replies
1.8k
views
Tutorial: Unsupervised clustering on gene expression data
gene RNA-seq expression clustering
11 weeks ago by Hamid Ghaedi 2.8k
41
votes
6
replies
15k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 10 months ago by ▴ 40 • written 20 months ago by 10k
141
votes
68
replies
41k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 5 months ago by • 0 • written 5.0 years ago by 84k
15
votes
2
replies
1.3k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 7 weeks ago by ▴ 780 • written 14 months ago by ▴ 270
194
votes
44
replies
67k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 8 weeks ago by 37k • written 10.2 years ago by 20k
6
votes
2
replies
908
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
15 months ago by Kevin Blighe 84k
0
votes
0
replies
797
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
16 months ago by mo • 0
2
votes
0
replies
1.4k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
16 months ago by Kevin Blighe 84k
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa tutorial Tutorial
updated 16 months ago by • 0 • written 10.7 years ago by ▴ 540
89
votes
104
replies
31k
views
24 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 8 weeks ago by ▴ 160 • written 4.3 years ago by 84k
0
votes
0
replies
647
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
17 months ago by Erin Haskell | ELIXIR ▴ 470
1
vote
0
replies
849
views
Tutorial: Slurm and parallelization
slurm
17 months ago by Juke34 7.4k
1
vote
0
replies
802
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
18 months ago by Pratik ▴ 850
12
votes
1
reply
1.7k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 18 months ago by ★ 14k • written 18 months ago by 84k
115
votes
66
replies
38k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera ENA fastq-dump Tutorial Fastq
5 months ago by ATpoint 66k
4
votes
0
replies
788
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
18 months ago by pbpanigrahi ▴ 420
0
votes
1
reply
649
views
Tutorial: Add Customized Filters in GDC
gdc
updated 18 months ago by 21k • written 18 months ago by ▴ 690
62
votes
26
replies
9.8k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 18 months ago by ▴ 180 • written 3.8 years ago by 15k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
18 months ago by jared.andrews07 ★ 14k
346 results • Page 1 of 7
Recent Votes
Comment: Automated way to pull representative/RefSeq genome using full species name?
Comment: Automated way to pull representative/RefSeq genome using full species name?
BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene symbols?
Answer: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene
BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene symbols?
A: Extract base information from aligned reads in a sam file
A: Extract base information from aligned reads in a sam file
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Scholar to Mensur Dlakic ★ 21k
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Recent Replies
Comment: Automated way to pull representative/RefSeq genome using full species name? by predeus ★ 1.8k
Hi Mirian, Thank you for your comment! I wanted to maybe avoid downloading all the bacterial species, and only download the assemblies an…
Comment: Transform Data into DNA picture by anasjamshed1994 ▴ 120
what does genotype mean in rsid? What does it indicate?![rsid][1] [1]: /media/images/7638ed2f-7ed2-4cc0-8ce4-58ab0226
Comment: Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me by hiroyuki.kato.911 • 0
Thanks! I got it!
Answer: Inquiry related to processing multiple db file simulataneously by Pierre Lindenbaum 151k
how about calling `dbDisconnect` after `dbGetQuery` ?
Answer: Automated way to pull representative/RefSeq genome using full species name? by MirianT_NCBI ▴ 340
Hi Alex, You can use [NCBI Datasets][1]. `datasets` allows users to download genome and associated annotation files as a data package. I…
Comment: bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detec by Pierre Lindenbaum 151k
but it's decoded AS a GFF/GTF file because bedtools can see columns 4 and 5 are integers. move columns 4 and 5 to columns 2 and 3 to create…
Comment: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene by Matthias Zepper 2.4k
I already linked the MANE website above. Navigate to *Accessing MANE data* and download [this file][1]. It is an equivalence table and cont…
Comment: bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detec by Simone • 0
It's not a GFF file, it's a TSV annotation file, output from BUSCO. The annotations are coordinates for BUSCO genes. I've tried using BEDOP…
Comment: What are Supplementary Reads? by cmdcolin ★ 2.5k
Large insertions or deletions can cause supplementary alignments to be created, even though it is still linear. But, minimap2 will try to a…
Comment: How to find rna strand direction before alignment? by swbarnes2 12k
OP said he didn't want to align. That script takes a bad and a bam as input.
Comment: GO enrichment analysis graphs after goseq: any easy solutions? by afsanarupa1 • 0
Please can you tell me details step by step how can these types of graphs be generated using output files from goseq as stated in trinity p…
Comment: What's Supplementary Reads? by Istvan Albert 96k
one concept the "linearity" of the alignment is important. A chimeric alignment is found to be "chimeric" if the entire read is represented…
Answer: How to find rna strand direction before alignment? by KoppesEA ▴ 80
[https://rseqc.sourceforge.net/][1] infer_experiment.py [1]: https://rseqc.sourceforge.net/ "RSEQC"
Answer: What's Supplementary Reads? by cmdcolin ★ 2.5k
I wrote a blogpost discussing some topics related to supplementary reads. Especially with long reads, supplementary reads are often "split …
Comment: For loop for aligning multiple paired end fastq files by Ram 37k
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