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Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 3 months ago by 40k • written 12 months ago by ▴ 20
1
vote
0
replies
588
views
Tutorial: Making LDA Score plot
LDA metagenomics
12 months ago by rohitsatyam102 ▴ 750
132
votes
123
replies
33k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 6 months ago by ★ 1.1k • written 4.9 years ago by 86k
11
votes
7
replies
9.1k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 4 months ago by 40k • written 2.6 years ago by ▴ 350
15
votes
1
reply
3.2k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 13 months ago by ★ 1.8k • written 20 months ago by 14k
84
votes
21
replies
18k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
27
votes
0
replies
3.2k
views
Tutorial: Building Docker images
singularity docker container
14 months ago by ATpoint 76k
2
votes
1
reply
40k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 14 months ago by 3.7k • written 14 months ago by ▴ 20
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 4 months ago by • 0 • written 5.3 years ago by ★ 1.3k
85
votes
2
replies
56k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 7 months ago by 40k • written 10.2 years ago by 11k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 6 months ago by 40k • written 5.8 years ago by ▴ 760
39
votes
8
replies
11k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
3
votes
2
replies
2.1k
views
Tutorial: Running fastq_screen on your data
fastqscreen
18 months ago by rohitsatyam102 ▴ 750
7
votes
14
replies
3.0k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 11 months ago by • 0 • written 19 months ago by ▴ 30
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 months ago by 40k • written 10.4 years ago by 9.7k
28
votes
13
replies
11k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 20 months ago by ★ 1.2k • written 23 months ago by 98k
4
votes
13
replies
11k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 3 months ago by 40k • written 4.6 years ago by ▴ 140
16
votes
9
replies
5.8k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 15 months ago by ▴ 70 • written 22 months ago by ★ 1.2k
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
20 months ago by Wayne ★ 1.8k
12
votes
4
replies
5.0k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 7 months ago by 40k • written 2.6 years ago by ▴ 130
27
votes
10
replies
70k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 6 months ago by 40k • written 2.5 years ago by ★ 1.4k
43
votes
6
replies
21k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 20 months ago by ▴ 40 • written 2.5 years ago by 12k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 29 days ago by ▴ 260 • written 5.8 years ago by 86k
15
votes
2
replies
1.8k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 11 months ago by ▴ 810 • written 2.0 years ago by ▴ 280
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 8 months ago by 40k • written 11.0 years ago by 20k
6
votes
2
replies
1.4k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.1 years ago by Kevin Blighe 86k
0
votes
0
replies
1.1k
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
2.1 years ago by mo • 0
2
votes
0
replies
2.5k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
2.2 years ago by Kevin Blighe 86k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 7 months ago by 40k • written 11.5 years ago by ▴ 540
93
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
0
votes
0
replies
929
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
2.3 years ago by Erin Haskell | ELIXIR ▴ 470
1
vote
0
replies
1.1k
views
Tutorial: Slurm and parallelization
slurm
2.3 years ago by Juke34 8.2k
1
vote
0
replies
1.1k
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
2.3 years ago by Pratik ▴ 910
13
votes
1
reply
2.5k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.3 years ago by ★ 15k • written 2.3 years ago by 86k
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 76k
4
votes
0
replies
1.1k
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
2.3 years ago by pbpanigrahi ▴ 420
0
votes
1
reply
913
views
Tutorial: Add Customized Filters in GDC
gdc
updated 2.3 years ago by 21k • written 2.3 years ago by ▴ 980
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 6 months ago by 40k • written 4.6 years ago by 16k
12
votes
20
replies
13k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 6 months ago by 40k • written 4.3 years ago by ★ 15k
4
votes
2
replies
2.2k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 6 months ago by 40k • written 4.3 years ago by ★ 9.3k
50
votes
14
replies
74k
views
10 follow
Tutorial: Using R in Conda
R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 750
33
votes
9
replies
30k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 6 months ago by 40k • written 3.1 years ago by ▴ 160
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 6 months ago by 40k • written 7.1 years ago by 26k
21
votes
2
replies
4.8k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 12 months ago by ▴ 40 • written 2.4 years ago by 8.2k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 6 months ago by 40k • written 3.4 years ago by 86k
82
votes
43
replies
30k
views
26 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 3 months ago by ▴ 40 • written 9.9 years ago by ★ 7.7k
8
votes
0
replies
2.4k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
2.5 years ago by rpolicastro 12k
238
votes
176
replies
88k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 4 months ago by 40k • written 8.2 years ago by ★ 4.7k
6
votes
0
replies
1.9k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
2.5 years ago by rpolicastro 12k
8
votes
1
reply
1.2k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 6 months ago by 40k • written 2.5 years ago by 86k
379 results • Page 2 of 8
Recent Votes
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
Answer: Unable to build applet in DNAnexus, .jar file not found
Comment: Spaceranger missing spatial coordinates [Discussion]
Answer: Low Alignment rate
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Recent Awards • All
Popular Question to bharata1803 ▴ 550
Teacher to GenoMax 134k
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Recent Replies
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject by Qi • 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis? by Yogi ▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions by Yogi ▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question by Istvan Albert 98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate by dsull ★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian) by morovatunc ▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes? by Michael 53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate by Mehwish • 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting by Ram 40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting by bk11 ★ 1.2k
I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
Comment: Violin plot (Monocle 3) - Troubleshooting by Ram 40k
What is the output to: ```r help.search('plot_genes_violin', agrep=FALSE, ignore.case=FALSE, fields=c('name')) lsf.str() sessionInfo() ```
Comment: Violin plot (Monocle 3) - Troubleshooting by seattlescientist_01 • 0
I see the error message but I'm confused on what it's telling me.
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