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384 results • Page 2 of 8
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4
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2
replies
1.9k
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Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
4 months ago by Dr.Animo ▴ 80
2
votes
0
replies
1.0k
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 5 months ago by 41k • written 11 months ago by ▴ 360
1
vote
0
replies
2.3k
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo R data-mining differential-gene-expression RNA-Seq
updated 5 months ago by 41k • written 11 months ago by ▴ 360
5
votes
0
replies
1.2k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 5 months ago by 41k • written 11 months ago by ▴ 360
6
votes
0
replies
3.4k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
9 months ago by Novogene ▴ 360
50
votes
1
reply
7.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 10 months ago by 41k • written 3.2 years ago by 78k
1
vote
3
replies
803
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
8 months ago by barslmn ★ 2.0k
73
votes
60
replies
26k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 10 months ago by 41k • written 6.2 years ago by 86k
14
votes
31
replies
6.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 9 months ago by 41k • written 4.3 years ago by 8.4k
1
vote
2
replies
1.3k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 5 months ago by 41k • written 14 months ago by ▴ 20
1
vote
0
replies
717
views
Tutorial: Making LDA Score plot
LDA metagenomics
14 months ago by rohitsatyam102 ▴ 780
132
votes
123
replies
35k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 months ago by ★ 1.1k • written 5.1 years ago by 86k
11
votes
7
replies
9.9k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 6 months ago by 41k • written 2.8 years ago by ▴ 360
15
votes
1
reply
3.5k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 15 months ago by ★ 1.8k • written 23 months ago by 14k
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 9 months ago by 41k • written 3.2 years ago by 3.1k
27
votes
0
replies
3.4k
views
Tutorial: Building Docker images
singularity docker container
16 months ago by ATpoint 78k
2
votes
1
reply
49k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 16 months ago by 3.8k • written 16 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 6 months ago by • 0 • written 5.5 years ago by ★ 1.3k
85
votes
2
replies
57k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by 41k • written 10.5 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 9 months ago by 41k • written 6.0 years ago by ▴ 770
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 9 months ago by 41k • written 3.2 years ago by 3.1k
3
votes
2
replies
2.4k
views
Tutorial: Running fastq_screen on your data
fastqscreen
20 months ago by rohitsatyam102 ▴ 780
7
votes
14
replies
3.3k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 13 months ago by • 0 • written 21 months ago by ▴ 30
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 10 months ago by 41k • written 10.6 years ago by 9.7k
28
votes
13
replies
12k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 22 months ago by ★ 1.3k • written 2.2 years ago by 99k
4
votes
13
replies
12k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 5 months ago by 41k • written 4.8 years ago by ▴ 140
16
votes
9
replies
6.3k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 18 months ago by ▴ 70 • written 2.0 years ago by ★ 1.3k
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
23 months ago by Wayne ★ 1.8k
12
votes
4
replies
5.1k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 10 months ago by 41k • written 2.8 years ago by ▴ 130
29
votes
10
replies
74k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 9 months ago by 41k • written 2.7 years ago by ★ 1.5k
44
votes
6
replies
23k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 22 months ago by ▴ 40 • written 2.7 years ago by 12k
148
votes
70
replies
48k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 3 months ago by ▴ 260 • written 6.0 years ago by 86k
15
votes
2
replies
1.9k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 14 months ago by ▴ 820 • written 2.2 years ago by ▴ 280
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 11 months ago by 41k • written 11.2 years ago by 20k
6
votes
2
replies
1.5k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.3 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
2.3 years ago by mo • 0
2
votes
0
replies
2.8k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
2.4 years ago by Kevin Blighe 86k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 9 months ago by 41k • written 11.7 years ago by ▴ 540
95
votes
105
replies
41k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 9 months ago by 41k • written 5.3 years ago by 86k
0
votes
0
replies
1.0k
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
2.5 years ago by Erin Haskell | ELIXIR ▴ 470
1
vote
0
replies
1.2k
views
Tutorial: Slurm and parallelization
slurm
2.5 years ago by Juke34 8.4k
1
vote
0
replies
1.2k
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
2.5 years ago by Pratik ▴ 980
13
votes
1
reply
2.7k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.5 years ago by ★ 16k • written 2.5 years ago by 86k
117
votes
66
replies
44k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 9 months ago by 41k • written 5.4 years ago by 78k
4
votes
0
replies
1.2k
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
2.5 years ago by pbpanigrahi ▴ 420
0
votes
1
reply
994
views
Tutorial: Add Customized Filters in GDC
gdc
updated 2.5 years ago by 21k • written 2.5 years ago by ★ 1.1k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 9 months ago by 41k • written 4.8 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 9 months ago by 41k • written 4.5 years ago by ★ 16k
4
votes
2
replies
2.3k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 9 months ago by 41k • written 4.5 years ago by ★ 9.3k
51
votes
14
replies
80k
views
10 follow
Tutorial: Using R in Conda
R
updated 9 months ago by 41k • written 3.4 years ago by ▴ 780
384 results • Page 2 of 8
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Comment: GATK GetPileupSummaries Java heap space
Answer: How to subtract variants from one VCF file to another?
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
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Recent Replies
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Pierre Lindenbaum 158k
> Asking for bed file is not a suitable option in the current scenario. ???????
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Manuel Sokolov Ravasqueira ▴ 100
they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Pierre Lindenbaum 158k
> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Manuel Sokolov Ravasqueira ▴ 100
thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)
Comment: Is interleaved Fastq files the same as interlaced fastq by rpolicastro 12k
This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…
Comment: Is interleaved Fastq files the same as interlaced fastq by RCMC • 0
Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Pierre Lindenbaum 158k
how about using the bed file of your targets....
Answer: LCA from BLAST output by Dunois ★ 2.4k
You should probably be using `MMseqs2`'s `taxonomy` module for this: [https://github.com/soedinglab/MMseqs2#taxonomy][1] . [1]: https:/…
Comment: autodock vina on mac by iamsmor • 0
thank you but ı am already follow this tutorial steps but at mgltools steps at the page but ı dont undertsand there isnot no enough explana…
Comment: How to create interval list from reference fasta or dict file? by Manuel Sokolov Ravasqueira ▴ 100
Hello @MatthewP , were you able to that for a fasta file for example? If you have a fasta file containing a targeted region, how to you ge…
Comment: WGCNA Dendrogram Branch missing from modules by andres.firrincieli 3.5k
I am not familiar with hdWGCNA but perhaps some modules are excluded because their genes are not expressed in a certain proportion of cells.
Comment: LCA from BLAST output by Michael 53k
If you know the lineage information is complete you could compare which columns are identical, however, there may be unranked levels in bet…
Comment: Is GeSeq currently unavailable? by GenoMax 136k
Email the developers listed on contact page: https://chlorobox.mpimp-golm.mpg.de/contact.html
Comment: Alternative to Gentrome? by GenoMax 136k
Curious as to what is `gentrome`? Genome decoy + transcriptome?
Comment: Java class error message when using BBDuk by GenoMax 136k
> I have cloned the bbmap Git Hub You are not using official repository then. BBMap is available from [**SourceForge**][1] or Bitbucket…
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