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Showing top results for tag:
R
•
reset
0
votes
0
replies
43
views
Sankey + dot plot
ontology
R
sankey
GO
gene
6 hours ago by
Sofia
• 0
0
votes
1
reply
189
views
Extracting column from one seurat object based on common column and adding to the other object
R
SEURAT
updated 2 days ago by
bk11
★ 2.9k • written 2 days ago by
Varun Gupta
★ 1.3k
1
vote
0
replies
137
views
News:
Landscape Genomics course in Poland (January 20-24)
R
LocalAdaptation
Sambada
LandscapeGenomics
LFMM
2 days ago by
carlopecoraro2
★ 2.6k
0
votes
0
replies
150
views
NeuronChat: identifyCommunicationPatterns_Neuron() error
R
NeuronChat
3 days ago by
sooni
▴ 20
1
vote
1
reply
199
views
Interpreting MA plot - DEG
R
DEG
ggplot2
updated 4 days ago by
Ram
44k • written 5 days ago by
NEWBIE
• 0
3
votes
2
replies
282
views
Understanding how champ.DMP determines the reference group for phenotypes
phenotype
ChAMP
champ.DMP
R
3 days ago by
Benjamin
▴ 10
0
votes
6
replies
360
views
Best practice for gene ontology/pathway/geneset enrichment in 10x data
R
Seurat
scRNA
updated 10 days ago by
jared.andrews07
★ 17k • written 10 days ago by
yura.grabovska
▴ 430
1
vote
1
reply
199
views
Conflict packages R
R
updated 10 days ago by
Ram
44k • written 10 days ago by
marco.barr
▴ 150
0
votes
2
replies
385
views
WGCNA: Problem with selecting soft threshold below R^2 0.8
R
network
WGCNA
updated 14 days ago by
LChart
4.3k • written 17 days ago by
emilymily77
• 0
0
votes
3
replies
360
views
installing ArchR on a mac
R
ArchR
updated 16 days ago by
Bastien Hervé
5.5k • written 16 days ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
213
views
News:
Metabolomics with R/Bioconductor Online Course
Metabolomics
Bioconductor
R
updated 13 days ago by
Ram
44k • written 17 days ago by
carlopecoraro2
★ 2.6k
0
votes
2
replies
299
views
Can we treat outliers as batch variables in linear modeling?
R
modeling
Outlier
linear
11 days ago by
aUser
▴ 30
0
votes
1
reply
221
views
How to draw a Manhattan diagram based on the gene names?
gwas
manhattan-plot
r
updated 18 days ago by
Ram
44k • written 18 days ago by
jienting0402
• 0
0
votes
0
replies
172
views
News:
Course: Metabarcoding in Microbial Ecology
R
Qiime2
Metabarcoding
Microbial-Ecology
19 days ago by
carlopecoraro2
★ 2.6k
0
votes
2
replies
429
views
Converting genome build from hg38 to hg19 using liftOver via bigsnpr - error fetching file
snp
bigsnpr
liftover
r
updated 20 days ago by
kaaz
• 0 • written 7 weeks ago by
dam4l
▴ 200
0
votes
1
reply
377
views
Help Needed: Importing and Analyzing GWAS Data from GWAS Catalog in R
R
GWAS
updated 20 days ago by
Ram
44k • written 23 days ago by
城玮
• 0
0
votes
0
replies
268
views
News:
Beyond Beginner R: Advancing Your Coding Skills (Sept 16-19, 2024)
R
Coding
Reproducibility
Programming
updated 23 days ago by
Ram
44k • written 23 days ago by
carlopecoraro2
★ 2.6k
0
votes
0
replies
584
views
Job:
2 x PhD / Doctoral position in Biomedical Data Sciences & Bioinformatics for studying human health and disease
R
PhD
Biomedicine
Data-Science
updated 23 days ago by
Ram
44k • written 24 days ago by
a_gruber
▴ 30
0
votes
0
replies
218
views
News:
Join Our Online Course: Reproducibility Data Analysis with R (28-31 October 2024)
R
Git
Quarto
Reproducibility
Docker
24 days ago by
carlopecoraro2
★ 2.6k
2
votes
0
replies
210
views
Plotting effects in Dirichlet regression
R
compositional-data
dirichlet-regression
updated 24 days ago by
Ram
44k • written 25 days ago by
Juan
▴ 30
6
votes
2
replies
4.9k
views
fgsea tutorial issue with BiocParallel
R
RNA-Seq
updated 25 days ago by
Assa Yeroslaviz
★ 1.9k • written 6.2 years ago by
1769mkc
★ 1.2k
4
votes
2
replies
274
views
GGTree flips my trees
R
ggtree
phylogenetics
25 days ago by
M.
▴ 40
0
votes
1
reply
193
views
Empty Results from champ.DMP Despite Expected Output
DMR
R
ChAMP
CpG
methylation
updated 5 days ago by
Basti
★ 2.0k • written 28 days ago by
Hiam
• 0
0
votes
0
replies
200
views
News:
Course in Italy: Introduction to Statistics in R (30 September to 3 October 2024)
R
GLM
Statistics
GLMM
4 weeks ago by
carlopecoraro2
★ 2.6k
5
votes
2
replies
303
views
How to Handle Unbalanced RNA-seq Data (710 vs. 15 Samples) Using DESeq2?
R
DESeq2
Unbalanced
RNA-seq
groups
updated 4 weeks ago by
Trivas
★ 1.8k • written 4 weeks ago by
Joe Kherery
▴ 140
2
votes
5
replies
444
views
How to View Peaks from ChIP-seq Data generated using old reference genome (hg18)
R
Peak
ChIP-seq
updated 4 weeks ago by
ATpoint
84k • written 4 weeks ago by
DareDevil
★ 4.3k
3
votes
9
replies
4.3k
views
6 follow
Error Muscle alignment (msa package, through Rscript)
msa
r
muscle
updated 5 weeks ago by
ulrich.bodenhofer
▴ 10 • written 4.4 years ago by
alnam
▴ 10
0
votes
0
replies
154
views
News:
Coding Courses @ Edinburgh Genomics
snakemake
python
R
workshop
linux
5 weeks ago by
Kat @ EdGe
▴ 10
1
vote
2
replies
1.4k
views
pathview - cannot open URL : HTTP status was '403 Forbidden'
R
kegg
pathview
updated 5 weeks ago by
lianchee11
▴ 50 • written 2.2 years ago by
Itamar
▴ 10
0
votes
0
replies
148
views
News:
Course - Introduction to R Shiny
R
Web-Applications
Shiny
5 weeks ago by
carlopecoraro2
★ 2.6k
1
vote
3
replies
349
views
What should I use correlate/compare microbiome compositional data to other data types
R
python
microbiome
compositional-biology
updated 5 weeks ago by
dthorbur
★ 2.4k • written 6 weeks ago by
Faith
▴ 50
1
vote
2
replies
295
views
R package to visualize multiple aligned chromatograms
R
plot
chromatogram
Sanger
5 weeks ago by
DaniCee
▴ 20
0
votes
3
replies
355
views
issue with terms label in Go dotplots
R
clusterProfiler
GO-terms
5 weeks ago by
G.S
▴ 60
0
votes
0
replies
184
views
News:
Course: Introduction to the Analysis of Longitudinal Data in Biology Using R
Longitudinal-Data
R
Epidemiology
Forecasting
Gene-Expression
updated 5 weeks ago by
Ram
44k • written 6 weeks ago by
carlopecoraro2
★ 2.6k
0
votes
5
replies
529
views
Differential gene expression (aiming to create heatmap) for raw RNAseq count data from different publications - how to?
R
DESeq2
Differential-expression
updated 6 weeks ago by
BioinfGuru
★ 2.1k • written 6 weeks ago by
Leah
• 0
1
vote
2
replies
352
views
topGO R package - how to account for fold expression and p value
R
proteomics
topGO
enrichment
6 weeks ago by
Sven
• 0
12
votes
5
replies
635
views
Forum:
Books and Blogs guiding the programming practice in bioinformatic research?
R
Python
Programming
6 weeks ago by
JustinZhang
▴ 100
2
votes
5
replies
400
views
Combining Overlapping ATC Code Usage in R
R
pharmacogenetics
6 weeks ago by
d.s.zimmerman
• 0
1
vote
1
reply
269
views
Testing for specific genes of whole RNA Sequencing
R
DESeq2
Sequencing
RNA
updated 6 weeks ago by
ATpoint
84k • written 6 weeks ago by
hagl
▴ 20
1
vote
11
replies
548
views
Use R to Produce CpG Information
R
CpG
5 weeks ago by
Dana
• 0
0
votes
0
replies
144
views
News:
course on Generalized Linear Mixed Models in R
R
Dharma
Mixed-Models
GLLM
6 weeks ago by
carlopecoraro2
★ 2.6k
4
votes
8
replies
511
views
Help in Log2 transform CPM count
R
edgeR
dge
Deseq2
updated 6 weeks ago by
Ram
44k • written 6 weeks ago by
G.S
▴ 60
2
votes
2
replies
463
views
Plotting LD heat map with plink.ld result
R
6 weeks ago by
selplat21
▴ 20
0
votes
2
replies
344
views
How to Fix "Error in checkForExperimentalReplicates(object, modelMatrix) :"?
DESeqDataSetFromMatrix
R
colData
DESeq2
RNA-Seq
6 weeks ago by
thatolivebranch
• 0
0
votes
1
reply
209
views
News:
A Practical Hands-On Introduction to R
Tidyverse
R
Data-Visualisation
Data-Analysis
ggplot2
updated 7 weeks ago by
noze
• 0 • written 7 weeks ago by
carlopecoraro2
★ 2.6k
1
vote
3
replies
328
views
DEG with several conditions
R
gene-expression
DESeq2
RNA-Seq
updated 7 weeks ago by
BioinfGuru
★ 2.1k • written 7 weeks ago by
Kylie
• 0
5
votes
11
replies
965
views
7 follow
why R scripts are preferred to biopython for RNA-Seq analyses?
R
Python
updated 7 weeks ago by
dariober
14k • written 8 weeks ago by
pinheirofabiano
▴ 90
0
votes
7
replies
2.0k
views
space converted into dots in header name
R
Rstudio
microbiome
updated 3.5 years ago by
cpad0112
21k • written 3.6 years ago by
Bioinfonext
▴ 470
0
votes
0
replies
166
views
How to choose the minGSsize and maxGSsize parameters in clusterProfilers GSEA
R
clusterProfiler
GSEA
7 weeks ago by
edoardofilippi1998
• 0
0
votes
0
replies
165
views
GDCRNATools: error in the gdcRNAMerge function
R
GDCRNATools
studioR
gdcRNAMerge
7 weeks ago by
Azra
▴ 10
50 results • Page
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Recent Votes
Answer: How to compile Multiz
Answer: Difference between GLM and Wilcoxon rank sum test
Answer: MarkDuplicatesSpark GATK flags for overcoming space issues
Answer: Numreads from samtools for Differential Expression
Comment: Numreads from samtools for Differential Expression
Answer: How to compile Multiz
C: How to make an intronic GTF for alignment
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Recent Replies
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz
by
GenoMax
145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz
by
Santex
• 0
I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
However, OE1_2 and OE1_3 are not the only groups experiencing problems. I tried another non-empty file, and: ``` rsem-calculate-expression …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
oops ``` file *.out.bam KO1_2Aligned.sortedByCoord.out.bam: gzip compressed data, extra field KO1_2Aligned.toTranscriptome.out.bam: …
Answer: Converting bam to sam using htslib C++ api
by
Pierre Lindenbaum
164k
read https://github.com/samtools/samtools/blob/develop/sam_view.c * allocate a new bam1_t* b = bam_init1 * open the input file: sam_op…
Comment: Converting bam to sam using htslib C++ api
by
Pierre Lindenbaum
164k
> 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…
Comment: FastQC and HISAT2
by
Jaber
• 0
Thank you, it worked almost after two months of struggle, I nearly deleted everything and reinstalled it, I assume the problem was someth…
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