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142 results • Page
1 of 3
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Rank
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Votes
Replies
7
votes
1
reply
153
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 2 days ago by
dariober
14k • written 2 days ago by
nhaus
▴ 360
5
votes
5
replies
618
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 5 days ago by
Mbofire
• 0 • written 14 days ago by
Ming Tommy Tang
★ 3.9k
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
14 days ago by
Kevin Blighe
87k
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 19 days ago by
ATpoint
82k • written 20 days ago by
BioinfGuru
★ 1.7k
7
votes
3
replies
2.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 20 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
1
vote
0
replies
204
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
21 days ago by
Novogene
▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 21 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
50
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 6 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
10
votes
6
replies
4.2k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 6 weeks ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
0
votes
0
replies
239
views
Tutorial:
Parsing HMMER output
HMMER
updated 6 weeks ago by
GenoMax
142k • written 6 weeks ago by
I0110
▴ 140
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 7 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 8 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
16k
46
votes
13
replies
15k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 8 weeks ago by
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
2
votes
0
replies
223
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
10 weeks ago by
Novogene
▴ 420
3
votes
0
replies
243
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
10 weeks ago by
Novogene
▴ 420
6
votes
0
replies
559
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by
zx8754
11k • written 3 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
334
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
1
vote
5
replies
641
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
3
votes
2
replies
559
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
2
votes
1
reply
443
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
1
reply
306
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
0
votes
0
replies
257
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
268
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
296
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
290
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
358
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
0
votes
0
replies
257
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
296
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
338
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
562
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
2
votes
0
replies
423
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
265
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
1
vote
1
reply
354
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
2
votes
3
replies
619
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
6
votes
1
reply
464
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
0
votes
0
replies
273
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 4 months ago by
Julia Ma
▴ 120
39
votes
16
replies
37k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
142k • written 3.7 years ago by
lavinia.gordon
▴ 160
1
vote
0
replies
359
views
Tutorial:
4 CITE-seq tutorials
CTIE-seq
4 months ago by
Ming Tommy Tang
★ 3.9k
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
sil_bioinfo
▴ 40 • written 8 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
385
views
Tutorial:
download metadata using GEOquery
computational-biology
GEO
metadata
updated 4 months ago by
Ram
43k • written 5 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
342
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
5 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
383
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
5 months ago by
rohitsatyam102
▴ 850
0
votes
0
replies
480
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
6 months ago by
rohitsatyam102
▴ 850
0
votes
4
replies
754
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
6 months ago by
Coremine Medical
▴ 20
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 6 months ago by
Ram
43k • written 10.6 years ago by
Irsan
★ 7.8k
1
vote
0
replies
533
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
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 6 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
2
votes
0
replies
579
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
0
votes
1
reply
547
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 8 months ago by
ATpoint
82k • written 8 months ago by
JC
▴ 30
4
votes
2
replies
2.9k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 8 months ago by
GenoMax
142k • written 4.0 years ago by
ATpoint
82k
142 results • Page
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What is Deepvariant default filtering values ?
Answer: Nextflow: how to get the process work dir, within the process
RNA-seq: Explain STAR quantMode geneCounts values
Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
Comment: Help with Biopython for Beginner
Comment: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
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Comment: How to convert normalized BigWig file to count matrix?
by
Pierre Lindenbaum
161k
bigwig is chrom/start/end/value . what kind of matrix do you want ?
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
I want to use the matrix derived from bigwig files to perform different analysis by DESeq2 or edgeR.
Answer: Have you ever obtained user guide of ExomeCNV?
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▴ 10
I have uploaded the ExomeCNV (v1.4) user manual [here][1]. [1]: https://fastupload.io/hZbU
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I assume you mean "server" as in local hardware that you own/control since "cloud" is a just bunch of servers on internet that you rent (pa…
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Comment: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
by
Pierre Lindenbaum
161k
> could you please explain what the collate does? http://www.htslib.org/doc/samtools-collate.html
Comment: ComBat_Seq stuck adjusting the data
by
Jaïr
• 0
Same keeps happening to me; but it is weird, I corrected the batch effect with the same exact function a few months ago and worked fine. I …
Comment: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
by
Lila M
★ 1.2k
Thank you for the feedback! I already used just the `samtools fastq -1 R1.fq.gz -2 R2.fq.gz -s Rx.fq.gz -0 R0.fq.gz`. Could you please exp…
Comment: Nextflow: how to get the process work dir, within the process
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…
Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
by
Pierre Lindenbaum
161k
faster use samtools collate+ fastq samtools collate -uOn128 in.bam TMPDIR | samtools fastq -1 R1.fq.gz -2 R2.fq.gz -s Rx.fq.gz -0 R…
Comment: Nextflow: how to get the process work dir, within the process
by
ScottDansk
▴ 10
legend thank you so much!
Answer: Nextflow: how to get the process work dir, within the process
by
Pierre Lindenbaum
161k
``` écho \${PWD} ``` <!-- where is Brian Brian is in the kitchen -->
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
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19k
What is the output of `samtools flagstat`?
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• 0
Hi, just a question, were you able to find a way to get it to work locally? My understanding from looking around seems to be at least so fa…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
Yoosef
▴ 60
Thanks a lot for your response. Today, I finally understood what my problem was. I have used CreateAssayObject function, while I should ha…
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