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121 results • Page 3 of 3
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Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 860
1
vote
1
reply
372
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
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370
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Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
368
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Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
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354
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
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0
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349
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Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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344
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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
1
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312
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
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0
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306
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
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304
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Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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304
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Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
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0
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289
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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288
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Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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284
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Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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270
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Tutorial: How to Label the Y Axis with percentage sign and Order Bars in ggplot2 using a single cell dataset
seurat single-cell ggplot2
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
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266
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Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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255
views
Tutorial: Parsing HMMER output
HMMER
updated 7 weeks ago by 142k • written 7 weeks ago by ▴ 140
3
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0
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250
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Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
11 weeks ago by Novogene ▴ 420
2
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0
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230
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Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
11 weeks ago by Novogene ▴ 420
1
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0
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220
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Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
28 days ago by Novogene ▴ 420
7
votes
1
reply
188
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 8 days ago by 14k • written 8 days ago by ▴ 360
121 results • Page 3 of 3
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Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
A: How To Merge Two Fastq.Gz Files?
Answer: Annotating file using bcftools
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Convert fastq.gz to fastq.bgz
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 10
Thanks a lot. It is almost what I need but not all. From your script, I can get information that how much degree different samples contri…
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame by Michael 54k
sorry, this isn't a sequence search but search by id ...
Comment: calculating genomic coverage/ base overlap in R by Sayantani • 0
![enter image description here][1]Hi, this is the list/ excel I am uploading ( coverage.xlsx ) ![enter image description here][1] [1…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by ATpoint 82k
There has been some spam bots in this thread which we cleaned up, you might still get notifications on it, just ignore.
Comment: Details on salmon index by ATpoint 82k
You're lucky that the senior developer @rob is often around, so you probably get your experts answer soon.
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by ATpoint 82k
I think the issue is that there is some contamination of groups. If you plot a PCA or MDS you see that there is a clear separation between …
Comment: What's next after GATK variant calling pipeline? by Michael 54k
The link didn't work for me. After getting variants from HaplotypeCaller, there are a lot of different options for follow-up analyses, but …
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p by ATpoint 82k
That having said, linked paper and its authors developed the csaw package over at Bioconductor that uses a window approach to avoid peak ca…
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p by Ian 6.0k
Really interesting answer. I had missed that paper and will digest it asap. I usually use DiffBind, but recently have been looking into p…
Comment: Annotating file using bcftools by kl ▴ 10
It worked with this `bcftools index -t $DATADIR/cpro_imputed_hrcgrch37.R2_0.3.vcf.gz` bcftools annotate \ -a $RefGenomes/All_2018…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
This is true. However, there are a number of studies that have done bioinformatics analysis in whole blood to see if there is a possibility…
Comment: ggrepel function: geom_text_repel() by sooni ▴ 20
Thank you for help! I solved the probelm with the package.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
I have checked the quality of the arrays using PCA and Boxplot (images attached) and some of the samples may deviate a little but perhaps n…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
the nt database was extracted, and this is latest version of nt database in ncbi and blastn with version 2.15. I used many query file.fast…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
they don't have clear answer for this problem. I run all subset of this data to find out error subsets database but it seem not any error i…
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