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19 results • Page
1 of 1
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0
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192
views
absolute path for symbolic links in Snakefile
Snakemake
updated just now by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
0
votes
2
replies
178
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 11 minutes ago by
Jesse
▴ 740 • written 2 days ago by
Broccoli
• 0
2
votes
3
replies
169
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 56 minutes ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
0
votes
2
replies
135
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
2 hours ago by
O.rka
▴ 710
0
votes
1
reply
117
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 15 hours ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
hagl
▴ 10
0
votes
2
replies
150
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
8 hours ago by
Guille
• 0
1
vote
1
reply
114
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 20 hours ago by
Gordon Smyth
★ 7.0k • written 22 hours ago by
pairedttest
▴ 10
2
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 19 hours ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
214
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
21 hours ago by
biocellbio
• 0
4
votes
8
replies
476
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 14 hours ago by
Alex Reynolds
35k • written 1 day ago by
J
▴ 10
4
votes
7
replies
536
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 12 hours ago by
dsull
★ 5.8k • written 4 days ago by
qudrat.nii
▴ 10
3
votes
0
replies
121
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 21 hours ago by
Ram
43k • written 1 day ago by
Claire Watson
▴ 60
0
votes
2
replies
190
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 21 hours ago by
Ram
43k • written 1 day ago by
The_PyPanda
▴ 10
0
votes
0
replies
97
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 21 hours ago by
Ram
43k • written 1 day ago by
SineWave
• 0
1
vote
3
replies
172
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 2 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
zihanss
• 0
1
vote
6
replies
328
views
ScRNA data question
scRNA
Vlnplot
Samples
7 hours ago by
starswillfade
▴ 10
0
votes
3
replies
252
views
Highest variable features in single cell data
single-cell
updated 22 hours ago by
bk11
★ 2.4k • written 2 days ago by
Kazo
• 0
3
votes
4
replies
356
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 5 hours ago by
BioinfGuru
★ 1.7k • written 2 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
5
replies
292
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 4 hours ago by
Istvan Albert
100k • written 3 days ago by
sehriban.buyukkilic
▴ 10
19 results • Page
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Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
How do I find out the read lenght of a fastq file?
Calculate Allele balance by sample
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
Answer: Is there a tool that sorts gtf files?
Answer: gvcf joint calling
Answer: Heatmap and rna-seq
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Recent Awards •
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Popular Question
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rohitsatyam102
▴ 850
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candron
▴ 10
Scholar
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Alex Reynolds
35k
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chaco001
▴ 40
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141k
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★ 1.7k
Recent Replies
Answer: absolute path for symbolic links in Snakefile
by
Jesse
▴ 740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
Jesse
▴ 740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
Comment: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
Arup Ghosh
3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
O.rka
▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
colindaven
6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question
by
starswillfade
▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling
by
zihanss
• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Guille
• 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq
by
dsull
★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
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