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142 results • Page
3 of 3
Sort: Views
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Views
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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
654
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
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
3
votes
1
reply
636
views
Tutorial:
Coordinate Systems and genomic variant description
coordinate-system
HGVS
normalization
VCF
updated 9 months ago by
Ram
43k • written 9 months ago by
Juke34
8.5k
1
vote
0
replies
627
views
Tutorial:
common mistakes in using spreadsheets
excel
spreadsheet
structured-data
updated 8 months ago by
Ram
43k • written 8 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
5
replies
605
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
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
7
votes
0
replies
590
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
8 months ago by
barslmn
★ 2.1k
2
votes
0
replies
562
views
Tutorial:
Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf
sparql
data-management
graph
updated 7 months ago by
Ram
43k • written 7 months ago by
Pierre Lindenbaum
161k
2
votes
3
replies
554
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis with DEseq2
python
pyDESeq2
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
1
reply
530
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
6
votes
0
replies
525
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 11 weeks ago by
zx8754
11k • written 11 weeks ago by
Ming Tommy Tang
★ 3.9k
3
votes
2
replies
525
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by
ATpoint
82k • written 3 months ago by
Julia Ma
▴ 120
0
votes
1
reply
524
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 7 months ago by
ATpoint
82k • written 7 months ago by
JC
▴ 30
0
votes
0
replies
517
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
1
vote
0
replies
509
views
Tutorial:
How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq
heatmap
rstats
TCGA
5 months ago by
Ming Tommy Tang
★ 3.9k
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
0
votes
0
replies
456
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
5 months ago by
rohitsatyam102
▴ 840
6
votes
1
reply
428
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
2
votes
0
replies
394
views
Tutorial:
Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
2
votes
1
reply
394
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq
space
clustering
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
363
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
5 months ago by
rohitsatyam102
▴ 840
0
votes
0
replies
351
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
1
vote
0
replies
332
views
Tutorial:
4 CITE-seq tutorials
CTIE-seq
4 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
326
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
1
reply
320
views
Tutorial:
Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING
ppi
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
0
replies
317
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
4 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
304
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
0
votes
0
replies
300
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
1
reply
285
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq
MetaTiME
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
0
replies
270
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
0
votes
0
replies
264
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
1
vote
0
replies
263
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq
SCSA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
248
views
Tutorial:
Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python
RNA-seq
batch-correction
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
241
views
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
1
vote
0
replies
239
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
0
votes
0
replies
239
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
0
votes
0
replies
224
views
Tutorial:
How to Label the Y Axis with percentage sign and Order Bars in ggplot2 using a single cell dataset
seurat
single-cell
ggplot2
3 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
0
replies
219
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
8 weeks ago by
Novogene
▴ 420
0
votes
0
replies
208
views
Tutorial:
Parsing HMMER output
HMMER
updated 4 weeks ago by
GenoMax
141k • written 4 weeks ago by
I0110
▴ 140
2
votes
0
replies
198
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
8 weeks ago by
Novogene
▴ 420
1
vote
0
replies
169
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
6 days ago by
Novogene
▴ 420
142 results • Page
3 of 3
Recent Votes
Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
A: Finding the centromere and telomere of cattle genome (Bos Taurus)
A: How to systematically check if a bam file is truncated
Comment: some error in building kraken2 database
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
C: RSeQC Output from infer_experiment.py - what does it mean?
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Recent Replies
Comment: To get p-values for the TPM
by
ATpoint
82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis
by
gv
• 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM
by
VITALA
• 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
dsull
★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file
by
samuelkalandarov2002
▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
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 and can be globally aligned; otherwise it is safer to compute local alignments (for…
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…
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