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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
592
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 5.0 years ago by 86k
11
votes
7
replies
9.2k
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 ▴ 360
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 21 months ago by 14k
84
votes
21
replies
19k
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
3.3k
views
Tutorial: Building Docker images
singularity docker container
14 months ago by ATpoint 77k
2
votes
1
reply
41k
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 10.3 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 ★ 1.3k • 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
22k
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 4 weeks ago by ▴ 260 • written 5.9 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
70k
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
932
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
2.6k
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 77k
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
914
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
75k
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 7.2 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
84
votes
47
replies
30k
views
28 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 3 days ago by 40k • written 10.0 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
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Recent Replies
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again... by GenoMax 134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files by Alex Reynolds 35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File by Reem • 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR by Trivas ★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files by GenoMax 134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools) by Pierre Lindenbaum 157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output by langziv ▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files by Pierre Lindenbaum 157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output by shelkmike ▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages by ATpoint 77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
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