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141 results • Page 2 of 3
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Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 6 days ago by • 0 • written 15 days ago by ★ 3.9k
5
votes
2
replies
3.1k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 12 months ago by 43k • written 7.1 years ago by ★ 9.4k
5
votes
13
replies
1.7k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 20 days ago by 82k • written 21 days ago by ★ 1.7k
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
4
votes
1
reply
1.9k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 11 months ago by 43k • written 6.7 years ago by ▴ 40
4
votes
0
replies
785
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
4
votes
0
replies
2.3k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 12 months ago by 43k • written 7.1 years ago by ▴ 100
4
votes
2
replies
1.1k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
9 months ago by Ming Tommy Tang ★ 3.9k
3
votes
3
replies
8.8k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 11 months ago by 43k • written 6.4 years ago by ▴ 100
3
votes
2
replies
2.7k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 12 months ago by 43k • written 7.0 years ago by ▴ 100
3
votes
3
replies
1.2k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 4 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
3
votes
4
replies
4.5k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 11 months ago by 43k • written 6.0 years ago by ★ 2.5k
3
votes
2
replies
561
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 82k • written 3 months ago by ▴ 120
3
votes
0
replies
2.2k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 11 months ago by 43k • written 6.3 years ago by 22k
3
votes
4
replies
3.6k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 11 months ago by 43k • written 5.5 years ago by ▴ 340
3
votes
2
replies
8.9k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 11 months ago by 43k • written 6.4 years ago by ★ 2.5k
3
votes
0
replies
749
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
10 months ago by Ming Tommy Tang ★ 3.9k
3
votes
0
replies
244
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
10 weeks ago by Novogene ▴ 420
3
votes
1
reply
3.4k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
updated 3 months ago by ▴ 120 • written 2.8 years ago by 87k
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 12 months ago by 43k • written 7.1 years ago by ▴ 30
3
votes
1
reply
2.3k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 12 months ago by 43k • written 6.9 years ago by ★ 1.6k
3
votes
1
reply
653
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 months ago by 43k • written 9 months ago by 8.6k
2
votes
0
replies
1.2k
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 5 months ago by • 0 • written 15 months ago by ★ 1.6k
2
votes
0
replies
1.4k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 11 months ago by 43k • written 5.9 years ago by ▴ 340
2
votes
0
replies
430
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
2
votes
0
replies
582
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 7 months ago by 43k • written 7 months ago by 161k
2
votes
0
replies
225
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
10 weeks ago by Novogene ▴ 420
2
votes
0
replies
6.9k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 11 months ago by 43k • written 6.4 years ago by ▴ 320
2
votes
0
replies
1.2k
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 10 months ago by 43k • written 16 months ago by ▴ 420
2
votes
0
replies
483
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
2
votes
0
replies
3.2k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
2
votes
0
replies
2.1k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 11 months ago by 43k • written 6.4 years ago by ★ 2.4k
2
votes
1
reply
449
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
0
replies
725
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 11 months ago by 43k • written 11 months ago by ▴ 20
2
votes
3
replies
2.7k
views
Tutorial: It's about the journey, and not the destination
R network
updated 12 months ago by 43k • written 7.1 years ago by ★ 1.2k
2
votes
3
replies
623
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
2
votes
0
replies
1.5k
views
Tutorial: Webinar: Extracting research evidence from publications
text-mining ontology pubmed
updated 11 months ago by 43k • written 6.2 years ago by ▴ 60
2
votes
0
replies
3.3k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 11 months ago by 43k • written 6.6 years ago by ★ 2.5k
1
vote
0
replies
207
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
22 days ago by Novogene ▴ 420
1
vote
0
replies
694
views
Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix scRNA-seq single-cell rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
1
vote
0
replies
1.7k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 12 months ago by 43k • written 6.8 years ago by ▴ 350
1
vote
0
replies
1.5k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.3 years ago by ▴ 90
1
vote
0
replies
693
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
1
vote
0
replies
360
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
536
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
6 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
644
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
1
vote
0
replies
361
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
2
replies
894
views
Tutorial: How to ask computational biology questions
computational-biology
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
1
vote
0
replies
298
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
4
replies
3.4k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 11 months ago by 43k • written 6.0 years ago by ▴ 340
141 results • Page 2 of 3
Recent Votes
Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
Truncated metadata file report from ENA Portal API
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Recent Replies
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message by Max • 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Giulio Genovese ▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic by GenoMax 142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list by i.sudbery 19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols by Ruqaiya • 0
What does the star mean then ?
Comment: RNA seq analysis by prifa ▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location by dthorbur ★ 1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic by GenoMax 142k
> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
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