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142 results • Page
3 of 3
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240
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Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq
SCSA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
303
views
Tutorial:
How to convert sra files to fastq files using parallelized fastq-dump
fastq
sra
3 months ago by
Ming Tommy Tang
★ 3.9k
7
votes
0
replies
590
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
8 months ago by
barslmn
★ 2.1k
0
votes
0
replies
666
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
10 months ago by
Coremine Medical
▴ 20
0
votes
0
replies
206
views
Tutorial:
Parsing HMMER output
HMMER
updated 4 weeks ago by
GenoMax
141k • written 4 weeks ago by
I0110
▴ 140
1
vote
0
replies
680
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
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
454
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
5 months ago by
rohitsatyam102
▴ 840
2
votes
0
replies
467
views
Tutorial:
Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering
gene-expression
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
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
Ali
• 0 • written 15 months ago by
firestar
★ 1.6k
0
votes
0
replies
3.6k
views
Tutorial:
SFA (Stochastic Frontier Analysis) STATA 14
R
updated 11 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
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 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
647
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling
R
Computational-Biology
10 months ago by
sinha.shriprakash
▴ 20
1
vote
0
replies
330
views
Tutorial:
4 CITE-seq tutorials
CTIE-seq
4 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
0
replies
765
views
Tutorial:
How to do GSEA in R for RNAseq data
gsea
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
263
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
516
views
Tutorial:
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome
rstats
spatial
single-cell
8 months ago by
Ming Tommy Tang
★ 3.9k
2
votes
0
replies
197
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
8 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
Ram
43k • written 6.4 years ago by
vimalkvn
▴ 320
1
vote
0
replies
316
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
4 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
2.6k
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 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
0
votes
0
replies
667
views
Tutorial:
T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq
TCR
single-cell
computational
biology
8 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
350
views
Tutorial:
download metadata using GEOquery
computational-biology
GEO
metadata
updated 4 months ago by
Ram
43k • written 4 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
362
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
5 months ago by
rohitsatyam102
▴ 840
4
votes
0
replies
2.3k
views
Tutorial:
Accurate prediction of active enhancers using PARE
ChIP-Seq
histone-modification
enhancer
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Sachin Pundhir
▴ 100
1
vote
0
replies
1.4k
views
Tutorial:
Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by
Ram
43k • written 6.3 years ago by
bdolin
▴ 90
1
vote
0
replies
238
views
Tutorial:
Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
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
Ram
43k • written 16 months ago by
Novogene
▴ 420
0
votes
0
replies
653
views
Tutorial:
How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
2
votes
0
replies
1.5k
views
Tutorial:
Webinar: Extracting research evidence from publications
text-mining
ontology
pubmed
updated 11 months ago by
Ram
43k • written 6.1 years ago by
Maria_Levchenko
▴ 60
0
votes
0
replies
1.4k
views
Tutorial:
Data Panel In R Commander
R
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
238
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq
SCSA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
0
replies
813
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 5 months ago by
Ram
43k • written 13 months ago by
Milad
▴ 10
3
votes
0
replies
729
views
Tutorial:
best practices for single-cell RNAseq analysis
cell
single
scRNAseq
10 months ago by
Ming Tommy Tang
★ 3.9k
5
votes
0
replies
1.6k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
3
votes
0
replies
2.2k
views
Tutorial:
Deep Learning for Cancer Immunotherapy
keras
tensorflow
updated 11 months ago by
Ram
43k • written 6.2 years ago by
Jeremy Leipzig
22k
1
vote
0
replies
602
views
Tutorial:
How to make a perfect heatmap using RNAseq data
heatmap
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
2.2k
views
Tutorial:
Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 11 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
1
vote
0
replies
269
views
Tutorial:
How to Use Biomart to Find Mouse Orthologs for Human Genes
ids
gene
bioconductor
3 months ago by
Ming Tommy Tang
★ 3.9k
2
votes
0
replies
3.2k
views
Tutorial:
use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene
slicer
fastq
splitter
updated 10 months ago by
Ram
43k • written 6.5 years ago by
chen
★ 2.5k
0
votes
0
replies
3.6k
views
Tutorial:
Park Test for Heteroskedasticity In R Commander
R
Park-Test
updated 11 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
1.6k
views
Tutorial:
MWD (Mackinnon, White And Davidson) In R
R
updated 11 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
1.6k
views
Tutorial:
PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 11 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
142 results • Page
3 of 3
Recent Votes
Read pair orientation : Illumina TruSeq Stranded mRNA library
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Interested in Spatial Omics?
Answer: Seurat merge and batch correction
Answer: Seurat merge and batch correction
Comment: Per base sequence content error in RNAseq analysis
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Comment: How to calculate identity percentage between proteins contained in a FASTA file?
by
b.contreras.moreira
▴ 170
This should work if you know your sequences are related, otherwise is safer to compute local alignments with BLAST
Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
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