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143 results • Page
3 of 3
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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
0
replies
684
views
Tutorial:
How to convert gene ids in R
computational-biology
gene-id
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
236
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
1
vote
0
replies
532
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
0
votes
0
replies
670
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
10 months ago by
Coremine Medical
▴ 20
1
vote
0
replies
178
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
11 days ago by
Novogene
▴ 420
4
votes
0
replies
953
views
Tutorial:
How to make a heatmap in R and deep understand it
heatmap
r
12 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
314
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
0
replies
3.1k
views
Tutorial:
Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test
R-Commander
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
1
vote
0
replies
1.7k
views
Tutorial:
Using Subversion to update /devel branch of Bioconductor package
bioconductor
subversion
updated 11 months ago by
Ram
43k • written 6.7 years ago by
Bohdan Khomtchouk
▴ 350
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
1
vote
0
replies
342
views
Tutorial:
4 CITE-seq tutorials
CTIE-seq
4 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
315
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
595
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
8 months ago by
barslmn
★ 2.1k
0
votes
0
replies
249
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
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
516
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
2
votes
0
replies
2.1k
views
Tutorial:
How to display Agilent CGH array in IGV
IGV
CGH
updated 11 months ago by
Ram
43k • written 6.4 years ago by
sacha
★ 2.4k
5
votes
0
replies
2.2k
views
Tutorial:
Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm
meme
parallel
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Alex Reynolds
35k
6
votes
0
replies
535
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 12 weeks ago by
zx8754
11k • written 12 weeks ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
465
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
5 months ago by
rohitsatyam102
▴ 850
1
vote
0
replies
274
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
1
vote
0
replies
684
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
217
views
Tutorial:
Parsing HMMER output
HMMER
updated 5 weeks ago by
GenoMax
141k • written 5 weeks ago by
I0110
▴ 140
1
vote
0
replies
326
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
4 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
273
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
257
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
2
votes
0
replies
209
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
9 weeks ago by
Novogene
▴ 420
3
votes
0
replies
225
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
9 weeks ago by
Novogene
▴ 420
1
vote
0
replies
635
views
Tutorial:
common mistakes in using spreadsheets
excel
spreadsheet
structured-data
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
0
replies
775
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
651
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
2
votes
0
replies
710
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 10 months ago by
Ram
43k • written 10 months ago by
Coremine Medical
▴ 20
2
votes
0
replies
474
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
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
677
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
371
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
5 months ago by
rohitsatyam102
▴ 850
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
0
votes
0
replies
1.3k
views
Tutorial:
In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence
cloud
dna
sequencing
updated 11 months ago by
Ram
43k • written 5.7 years ago by
corlinp
• 0
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
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
2
votes
0
replies
408
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
1
vote
0
replies
250
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
143 results • Page
3 of 3
Recent Votes
A: vcf calculation of allele counts and allele number
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
which tool/software/package should I use to preprocess the rosetta-merck microarray platform raw data?
Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
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Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous
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trausch
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For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
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Thats very intersting! What are the features in your classifier?
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
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hagl
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Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
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I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
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Lluís R.
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Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
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ATpoint
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Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
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Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
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I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
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You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
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Fascinating! We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
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See the section on non full rank design matrices in the DESeq2 manual. In this case your problem is that healthy and 0dpi samples are e…
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Can you clarify what you mean by "100% of reads pass cutadapt, even though 70% of reads contain adapters and get trimmed. " did you set a m…
Comment: NGS forensics: how to know if data is fabricated
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I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
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Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
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Try using this library [GEOparse][1] [1]: https://github.com/guma44/GEOparse
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