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353 results • Page 1 of 8
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174
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Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
10 days ago by firestar ★ 1.5k
10
votes
7
replies
782
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 days ago by barslmn ★ 1.2k
1
vote
1
reply
262
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 22 days ago by 152k • written 22 days ago by ★ 1.2k
1
vote
0
replies
241
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
rRNA RNAmmer Annotation Genome
4 weeks ago by Dr.Animo ▴ 40
0
votes
0
replies
324
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo mining enrichment data Gene pathway RNA-Seq R
5 weeks ago by Novogene ▴ 210
0
votes
0
replies
427
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo mining differential data expression RNA-Seq gene R
5 weeks ago by Novogene ▴ 210
1
vote
0
replies
243
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo mining datasets data SRA RNA-Seq
5 weeks ago by Novogene ▴ 210
1
vote
0
replies
335
views
Tutorial: Gene Expression Omnibus Data Mining (IA): Quick and easy download of GEO data
geo mining data RNA-Seq R
6 weeks ago by Novogene ▴ 210
41
votes
1
reply
5.8k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger tutorial rna-seq
6 weeks ago by ATpoint 68k
1
vote
3
replies
353
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbs sampling splice
updated 7 weeks ago by 125k • written 7 weeks ago by ★ 1.2k
76
votes
19
replies
68k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools bcftools htslib Tutorial
updated 11 days ago by • 0 • written 4.5 years ago by ▴ 520
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 9 weeks ago by • 0 • written 5.4 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 12 weeks ago by 125k • written 6.9 years ago by 20k
12
votes
31
replies
4.5k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
gene geneset abinitio Tutorial genome
3 months ago by Juke34 7.5k
1
vote
2
replies
404
views
Tutorial: ViennaRNA package installation in Windows
install mfold viennarna rna windows
updated 4 months ago by 9.5k • written 4 months ago by ▴ 20
1
vote
0
replies
247
views
Tutorial: Making LDA Score plot
LDA metagenomics
4 months ago by rohitsatyam102 ▴ 690
128
votes
122
replies
27k
views
23 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 5 months ago by • 0 • written 4.3 years ago by 84k
9
votes
7
replies
5.1k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 5 months ago by • 0 • written 23 months ago by ▴ 210
11
votes
1
reply
2.0k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 5 months ago by ★ 1.8k • written 13 months ago by 14k
13
votes
8
replies
2.4k
views
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
11 weeks ago by ATpoint 68k
79
votes
21
replies
13k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment Tutorial GSEA RNA-Seq
7 weeks ago by Hamid Ghaedi 2.8k
3
votes
0
replies
431
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
5 months ago by Kevin Blighe 84k
27
votes
0
replies
2.5k
views
Tutorial: Building Docker images
singularity docker container
6 months ago by ATpoint 68k
1
vote
1
reply
12k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 6 months ago by ★ 2.5k • written 6 months ago by ▴ 10
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 6 months ago by 37k • written 4.6 years ago by ★ 1.3k
78
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 9.6 years ago by 11k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr gene RNA-Seq R Tutorial
updated 9 months ago by 84k • written 5.2 years ago by ▴ 740
1
vote
1
reply
1.1k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
TCGA Counts v32.0 Biolinks GDC STAR
updated 8 weeks ago by • 0 • written 9 months ago by ★ 1.7k
37
votes
8
replies
8.7k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer Tutorial R methylation
updated 9 weeks ago by ★ 1.1k • written 2.3 years ago by 2.8k
3
votes
2
replies
1.1k
views
Tutorial: Running fastq_screen on your data
fastqscreen
10 months ago by rohitsatyam102 ▴ 690
7
votes
14
replies
1.8k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 3 months ago by • 0 • written 11 months ago by ▴ 30
74
votes
14
replies
13k
views
15 follow
Tutorial: List Of Bioinformatics Books
bioinformatics tutorial books Tutorial
updated 4 months ago by 37k • written 9.7 years ago by 9.5k
24
votes
13
replies
5.7k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 12 months ago by ★ 1.1k • written 15 months ago by 96k
3
votes
13
replies
8.9k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf merge bcftools Tutorial
written 4.0 years ago by ▴ 140
13
votes
9
replies
3.6k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 7 months ago by ▴ 40 • written 14 months ago by ★ 1.1k
2
votes
0
replies
908
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell Biology R Computational signalling
13 months ago by sinha.shriprakash ▴ 20
0
votes
0
replies
7.7k
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
13 months ago by Wayne ★ 1.6k
12
votes
4
replies
4.3k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Tutorial linux bioinformatics R
updated 14 months ago by • 0 • written 24 months ago by ▴ 120
24
votes
10
replies
55k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
Tutorial error software R
updated 8 months ago by • 0 • written 22 months ago by ★ 1.3k
6
votes
2
replies
2.1k
views
Tutorial: Unsupervised clustering on gene expression data
gene RNA-seq expression clustering
4 months ago by Hamid Ghaedi 2.8k
41
votes
6
replies
17k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 12 months ago by ▴ 40 • written 22 months ago by 11k
142
votes
68
replies
42k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 7 months ago by • 0 • written 5.2 years ago by 84k
15
votes
2
replies
1.3k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 3 months ago by ▴ 790 • written 16 months ago by ▴ 270
194
votes
44
replies
67k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 25 days ago by 37k • written 10.4 years ago by 20k
6
votes
2
replies
972
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
17 months ago by Kevin Blighe 84k
0
votes
0
replies
842
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
18 months ago by mo • 0
2
votes
0
replies
1.6k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
18 months ago by Kevin Blighe 84k
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa tutorial Tutorial
updated 18 months ago by • 0 • written 10.8 years ago by ▴ 540
92
votes
105
replies
32k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 3 days ago by ▴ 40 • written 4.4 years ago by 84k
0
votes
0
replies
702
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
19 months ago by Erin Haskell | ELIXIR ▴ 470
353 results • Page 1 of 8
Recent Votes
Comment: RNA seq analysis from the data file which received from company
Answer: Multiple sequence alignment of sequenecs of different length
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Comment: Alien-hunter outputs
Answer: Annotating ENS codes to gene name
Comment: Annotating ENS codes to gene name
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Recent Replies
Comment: want the codes for Deseq2 to perform DEGs. by rupali • 0
thanks for help
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11 by Yingying • 0
Hi, Yes I've uploaded the diagnostic file to 10x support already, but haven't got any response yet.
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11 by GenoMax 125k
You may want to contact 10x tech support. When this process failed it must have created a diagnostic archive. You also get a message about …
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files? by jv ▴ 780
`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: Alien-hunter outputs by schlogl ▴ 130
@GenoMax Hope this helps...Thank you
Comment: DESeq2 results function runs very slow on Windows 10 by ATpoint 68k
Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file by ibq.enriquepola • 0
enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1 NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe by Chris ▴ 60
Thank you for your help! I got an error that I could not find the solution on the Internet: library(EnhancedVolcano) Loading required…
Comment: HTSeq error processing GFF file by barslmn ★ 1.2k
I guess you can try to replace the "?" to a "." Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10 by Istvan Albert 96k
Note the following: https://support.bioconductor.org/p/115415/ it looks like it has to do with the Parallel=TRUE flag
Comment: DESeq2 results function runs very slow on Windows 10 by GenoMax 125k
> there is a massive difference in performance between them. It still is taking only one minute.
Comment: HTSeq error processing GFF file by ibq.enriquepola • 0
Yes, ![enter image description here][1] [1]: /media/images/76ecd9a7-10c2-4526-9849-062605ca
Answer: How can I convert this pairwise format to fasta? by GenoMax 125k
This seems to be the output from `sam2pairwise` program: https://github.com/mlafave/sam2pairwise A quick/dirty way may be $ grep -A 1…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe by Basti ★ 1.3k
EnhancedVolcano(CV.markers, x = "avg_log2FC", y = "p_val", lab = rownames(CV.markers), pCutoff = 1e-4, FCcutoff =…
Comment: How to perform multiple comparisons using edgeR? by ryandward • 0
Actually, you get one FDR per gene if you don't loop, and perform the comparisons all at once.
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