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117 results • Page 2 of 3
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8
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Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 12 months ago by 37k • written 9.2 years ago by ★ 2.6k
9
votes
7
replies
5.0k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 4 months ago by • 0 • written 23 months ago by ▴ 210
10
votes
7
replies
751
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
4 days ago by barslmn ★ 1.2k
11
votes
6
replies
4.5k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 6 months ago by 37k • written 7.0 years ago by ★ 4.1k
60
votes
6
replies
8.8k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line tools bioinformatics Tutorial
updated 11 weeks ago by 37k • written 9.5 years ago by 9.5k
29
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 4 months ago by 37k • written 10.8 years ago by 96k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 10 months ago by 37k • written 8.8 years ago by ★ 1.8k
16
votes
5
replies
8.3k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
biomart perl api tutorial Tutorial
updated 4 months ago by 37k • written 10.4 years ago by 20k
53
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 4 months ago by 37k • written 9.2 years ago by ★ 1.2k
63
votes
5
replies
6.6k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 3 months ago by 37k • written 7.5 years ago by 12k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr gene RNA-Seq R Tutorial
updated 8 months ago by 84k • written 5.2 years ago by ▴ 740
34
votes
4
replies
5.5k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 11 weeks ago by 37k • written 7.5 years ago by ▴ 370
8
votes
3
replies
2.4k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 6 months ago by 37k • written 7.0 years ago by 23k
17
votes
3
replies
11k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 6 months ago by 37k • written 7.0 years ago by ★ 9.2k
10
votes
3
replies
1.5k
views
Tutorial: FASTA file split
Tutorial split fasta tutorial
7 months ago by Juke34 7.5k
1
vote
3
replies
347
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbs sampling splice
updated 6 weeks ago by 125k • written 6 weeks ago by ★ 1.2k
13
votes
3
replies
4.6k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 8 months ago by 37k • written 7.9 years ago by ▴ 860
0
votes
3
replies
2.3k
views
Tutorial: Automatic Primer Design
Assembly sequence
updated 5 months ago by 37k • written 7.2 years ago by ▴ 40
10
votes
3
replies
4.1k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 10 days ago by 37k • written 8.4 years ago by ▴ 860
1
vote
2
replies
2.8k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 3 months ago by 37k • written 7.5 years ago by ▴ 10
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
18
votes
2
replies
9.5k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 10 months ago by 37k • written 8.3 years ago by ▴ 860
3
votes
2
replies
1.1k
views
Tutorial: Running fastq_screen on your data
fastqscreen
10 months ago by rohitsatyam102 ▴ 690
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 6 months ago by 37k • written 7.0 years ago by ★ 1.8k
6
votes
2
replies
3.6k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
variant filtration vcf genotype genome Tutorial
11 months ago by kirannbishwa01 ★ 1.5k
1
vote
2
replies
394
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
21
votes
2
replies
3.3k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 4 months ago by ▴ 40 • written 21 months ago by 7.5k
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
2
replies
2.7k
views
Tutorial: Introduction to bedtools.
bedtools tutorial Tutorial
updated 11 months ago by 37k • written 8.2 years ago by 11k
8
votes
2
replies
6.2k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 12 months ago by 37k • written 8.2 years ago by 12k
0
votes
2
replies
2.4k
views
Tutorial: Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer' on 25 Feb
SNP cancer gene-regulation multiomics rna-seq
updated 9 months ago by 37k • written 8.0 years ago by ▴ 70
14
votes
2
replies
6.0k
views
Tutorial: ChIP-seq analysis tutorial
Tutorials ChIP-Seq
updated 4 months ago by 37k • written 7.4 years ago by ★ 2.9k
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
10
votes
2
replies
3.1k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 5 months ago by 37k • written 7.2 years ago by 20k
14
votes
2
replies
2.6k
views
Tutorial: Methylation Analysis Tutorial in R_part2
RNA-Seq R methylation Tutorial cancer
4 months ago by Hamid Ghaedi 2.8k
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 7 weeks ago by • 0 • written 9 months ago by ★ 1.7k
2
votes
1
reply
2.7k
views
Tutorial: Scripting for Biology - Online Virtual Classroom-based Module
perl python GO class
updated 4 months ago by 37k • written 7.4 years ago by ★ 1.1k
1
vote
1
reply
252
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 19 days ago by 152k • written 19 days ago by ★ 1.2k
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
5
votes
1
reply
3.9k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 6 weeks ago by 37k • written 7.6 years ago by 7.7k
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 12 months ago by 14k
22
votes
1
reply
2.9k
views
Tutorial: Introduction To R Course Materials Available
R
updated 27 days ago by 37k • written 10.8 years ago by 26k
12
votes
1
reply
4.7k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 3 months ago by 37k • written 7.5 years ago by 3.5k
12
votes
1
reply
4.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
RNA-Seq CITE-seq-count Tutorial scRNA-seq
5 months ago by colindaven 4.4k
1
vote
1
reply
11k
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
1
vote
0
replies
2.9k
views
Tutorial: Canadian Bioinformatics Workshops 2016 Series
Assembly SNP RNA-Seq ChIP-Seq alignment
updated 7 months ago by 37k • written 7.0 years ago by ▴ 30
12
votes
0
replies
7.2k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 9 months ago by 37k • written 8.0 years ago by ★ 4.6k
1
vote
0
replies
317
views
Tutorial: Gene Expression Omnibus Data Mining (IA): Quick and easy download of GEO data
geo mining data RNA-Seq R
5 weeks ago by Novogene ▴ 210
1
vote
0
replies
216
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
rRNA RNAmmer Annotation Genome
26 days ago by Dr.Animo ▴ 40
3
votes
0
replies
1.8k
views
Tutorial: Live webinar on 25 June: Copy Number Detection in Inherited Disorders and Somatic Cancer
copy-number-analysis strand-ngs cnv DNA-seq tumor
updated 27 days ago by 37k • written 7.7 years ago by ▴ 70
117 results • Page 2 of 3
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Answer: Looking for a tool which provides mapping quality score distributions from BAM f
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: Gviz python alternative
Answer: Gviz python alternative
Answer: Annotating snps with gene information
Comment: Plotting Correlation matrix
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Recent Replies
Answer: Python Dictionary of Primer3-py Primer Designs by barslmn ★ 1.2k
You're so close. You can simply loop over sequence dictionaries like you did with the `design_output` and check if the keys with `startswit…
Comment: Unable to install clusterProfiler on Mac M1 by GenoMax 125k
Have you installed `Xcode` and the command line tools that go with? If not you will need to install those.
Answer: SRA taxonomy analysis by Steve • 0
Thanks @genomax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/ I wonder if it …
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives? by demoraesdiogo2017 ▴ 80
thanks! however, shouldn't it also have a gtf/gff file with the annotations?
Comment: Getting a VCF file from plink .bed, .fam and .bim files by hi.there • 0
Thanks Ram. Yes. I have read all of this documentation before. --file and --bfile. I have actually tried doing the complete liftover be…
Answer: SRA taxonomy analysis by GenoMax 125k
This data may only be available using `BigQuery` for [**SRA in cloud**][1]. For more information on querying: https://www.ncbi.nlm.nih.g…
Comment: MesKit error message - Join columns must be present in data. by CH1374 • 0
column names for the maf are: [1] "Hugo_Symbol" "Chromosome" "Start_Position" [4] "End_Position" "Variant_Classification" "Variant_Type" [7…
Answer: scaffold assembly inro chromosomal assembly using reference genome by samuel.a.odonnell ▴ 450
Have a look at ragtag and ragout. I use ragout for smaller assemblies (~20 Mb and less) and ragtag for larger genomes.
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl by Ram 37k
I've been meaning to work on a Biostars-specific code formatting manual for a while now but the basic is pretty simple: You can use backtic…
Comment: Multiline Fasta To Single Line Fasta by Onur • 0
Thank you it's also worked for me too. Best,
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl by Estefania ▴ 10
Thanks Ram. Could you point to a manual on how to make the post look like yours? I just copy-pasted my R script and this is how it shows in…
Comment: extracting input files form Seurat by rasing02 • 0
Thank you jared.andrews07
Comment: extracting input files form Seurat by rasing02 • 0
Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature p…
Comment: Downloading 450k methylation data from GEO by GenoMax 125k
I don't think they have provided processed data as a single upload.
Answer: extracting input files form Seurat by jared.andrews07 ★ 14k
You can get the data behind any of the plots easily enough: ``` p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by…
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