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191 results • Page
4 of 4
Sort: Votes
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0
votes
10
replies
512
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 4 days ago by
i.sudbery
19k • written 12 days ago by
Patadu94
• 0
0
votes
0
replies
132
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
4 days ago by
Bine
▴ 60
0
votes
3
replies
282
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 4 days ago by
GenoMax
142k • written 4 days ago by
kim
• 0
0
votes
0
replies
125
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 4 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
129
views
barcode of TCR-sequencing
barcode
4 days ago by
yueli7
▴ 250
0
votes
0
replies
124
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 4 days ago by
Ram
43k • written 4 days ago by
Alexandros
• 0
0
votes
0
replies
161
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 4 days ago by
Ram
43k • written 4 days ago by
Chakri
• 0
0
votes
3
replies
389
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
4 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
224
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Dora
▴ 10
0
votes
1
reply
166
views
unable to get feature count results
featureCounts
updated 4 days ago by
Ram
43k • written 4 days ago by
Ravita
• 0
0
votes
3
replies
276
views
KEGG Pathways
r
RNA-seq
updated 3 days ago by
Ram
43k • written 4 days ago by
Sudip
• 0
0
votes
8
replies
436
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 3 days ago by
LauferVA
4.2k • written 5 days ago by
jinyu
▴ 10
0
votes
0
replies
141
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
3 days ago by
O.rka
▴ 710
0
votes
1
reply
589
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 3 days ago by
Ram
43k • written 3 days ago by
Dr Huma Naz
• 0
0
votes
1
reply
178
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Edmond
• 0
0
votes
0
replies
102
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
3 days ago by
VITALA
• 0
0
votes
5
replies
359
views
Telescope issue
Telescope
RNA-seq
updated 3 days ago by
GenoMax
142k • written 3 days ago by
eleven11
• 0
0
votes
1
reply
213
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 2 days ago by
Adam
▴ 30 • written 3 days ago by
J
• 0
0
votes
1
reply
140
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 2 days ago by
Ram
43k • written 3 days ago by
ernestine.kubi
• 0
0
votes
1
reply
174
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 2 days ago by
Adam
▴ 30 • written 4 days ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
94
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
2 days ago by
meck
• 0
0
votes
0
replies
121
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 2 days ago by
Ram
43k • written 2 days ago by
Oscar
▴ 10
0
votes
1
reply
199
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 2 days ago by
GenoMax
142k • written 2 days ago by
mgranada3
▴ 30
0
votes
1
reply
581
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 2 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
0
replies
92
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
2 days ago by
James
▴ 10
0
votes
1
reply
267
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 2 days ago by
Scooter
▴ 280 • written 8 days ago by
avocado123
• 0
0
votes
0
replies
94
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
2 days ago by
Vijith
▴ 30
0
votes
0
replies
83
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
2 days ago by
Rhiannon
• 0
0
votes
0
replies
95
views
Use of annotation of integrated Seurat object in single sample
Seurat
2 days ago by
Bine
▴ 60
0
votes
1
reply
216
views
Subsetting and merging back Seurat Object brings different results
Seurat
2 days ago by
Bine
▴ 60
0
votes
0
replies
99
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
774
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 2 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
502
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 2 days ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
2
replies
158
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
1
reply
140
views
Provean help
variant
Provean
updated 1 day ago by
Mensur Dlakic
★ 27k • written 2 days ago by
Arun Sai Kumar
• 0
0
votes
1
reply
146
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 1 day ago by
anovak
▴ 120 • written 2 days ago by
Hang
• 0
0
votes
7
replies
515
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 1 day ago by
LChart
3.9k • written 5 days ago by
kl
▴ 10
0
votes
1
reply
185
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 1 day ago by
Chris Dean
▴ 390 • written 1 day ago by
sovrappensiero
▴ 90
0
votes
2
replies
688
views
homer not configured properly
Homer
makeTagDirectory
updated 1 day ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
0
votes
1
reply
542
views
HOMER on AWS
HOMER
updated 1 day ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
103
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
1 day ago by
Jeyong
• 0
191 results • Page
4 of 4
Recent Votes
Answer: Design matrix Differential expression analysis
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Answer: RNA velocity for smart-seq2 dataset
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Recent Replies
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
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