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24 results • Page
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1
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1.2k
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News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
12 days ago by
Zhenyu Zhang
★ 1.2k
0
votes
2
replies
425
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
3 days ago by
David Langenberger
11k
1
vote
2
replies
277
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 10 days ago by
Weiwen
• 0 • written 11 days ago by
MICOS
▴ 10
3
votes
0
replies
240
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 20 days ago by
Ram
43k • written 21 days ago by
Claire Watson
▴ 60
0
votes
0
replies
222
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 28 days ago by
Ram
43k • written 29 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
204
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 28 days ago by
Ram
43k • written 29 days ago by
carlopecoraro2
★ 2.5k
1
vote
0
replies
200
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
15 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
187
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 21 days ago by
Ram
43k • written 21 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
180
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 16 days ago by
Ram
43k • written 16 days ago by
Chakri
• 0
0
votes
0
replies
164
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 25 days ago by
Ram
43k • written 26 days ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
155
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
7 days ago by
carlopecoraro2
★ 2.5k
3
votes
0
replies
154
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 23 days ago by
Ram
43k • written 23 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
147
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 22 days ago by
Ram
43k • written 23 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
146
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
14 days ago by
Amos Bairoch
▴ 120
0
votes
0
replies
144
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 17 days ago by
Ram
43k • written 17 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
136
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
18 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
128
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
126
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 8 days ago by
Ram
43k • written 8 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
125
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
25 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
122
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 14 days ago by
Ram
43k • written 15 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
120
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
12 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
119
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
9 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
85
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
2 days ago by
Transmitting Science communication
▴ 70
0
votes
0
replies
82
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 13 hours ago by
Ram
43k • written 20 hours ago by
carlopecoraro2
★ 2.5k
24 results • Page
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Recent Votes
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
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